Chuck Vs The Body Thief
by MissMonk
Summary: The Government has found a solution to the instability of the Intersect caused by Chuck Bartowski's emotions. Delete him with Intersect 3.0.
1. Chapter 1

A/N: None of this is real, I have no clue if any of it is possible, everything is made up and BSed through in order to make an enjoyable story.

Chapter 1

Chuck groaned as his mind came to consciousness. His head hurt. Really hurt. As in pounding on a brick wall with ice picks hurt. He was afraid to move in fear of the pain, afraid that the already unbearableness of it would escalate further.

He didn't know where he was, and at the moment he really didn't care. He was aware enough to know that he should be bothered by that but at the moment his only concern was to hold still, to not move. Keeping his eyes closed Chuck forced his mind to stop thinking, thoughts exacerbating the white hot pain that stabbed at his brain.

After a few moments though he thought better of it and decided to move a little to see if that would help abate his pain. Moving an inch however to release his arm that was trapped under his body that he could barely feel at this time dissuaded him from that course of action. Nausea rose through his stomach and up to his throat. His head which pounded in time with his heart caused dizziness making him scrunch his eyes closed tighter hoping to stop himself before he threw up.

"You will feel better if you expel the contents." A voice inside his head echoed, causing him to groan. He was confused for second at the voice, not sounding like his normal internal one. That moment of confusion was all his body needed to let go and stop fighting its instincts to keep everything in.

Chuck quickly rose on his arms and bent over the side of where he was and expelled whatever contents were in his stomach. His eyes closed tightly his head pounded as his body proceeded. After what felt like eternity it finally stopped and he took deep breaths to calm his racing heart.

Falling on his side on something soft he panted and curled up in a ball as tight as his lanky body would let him, his body now aching to add to his migraine. He shivered as he wrapped his arms around his body as chills raged all across his body causing bumps to appear and the hairs on his skin to stand up.

The last thing he knew before losing consciousness was something cool being placed on his forehead and soothing words inside his mind telling him to sleep.

"That's disgusting." Casey grunted grimacing at the mess in the bucket his partner had made. He made eye contact with his other partner Sarah Walker as he removed it from the side of the bed Chuck was lying on. He opened the door on the other side of the room and handed it out to the guard with directions to get rid of it and grab another bucket.

Turning back he crossed his arms in front of his chest, standing guard as Sarah took a cool rag she had gotten from the adjacent bathroom.

"This is the worse update he's had." Sarah commented, cleaning around his face. "I don't think we can move him."

Casey grunted his agreement. He wasn't planning on moving the kid in the first place especially since they arrived at this CIA facility in his car. Still he agreed with her on her assessment. He can't deny, as much as he wants to that the updates the CIA and NSA have Chuck go through to keep his information refreshed are brutal. He can't imagine having all that data being written inside his head like that. And watching Chuck go through it, on an increased basis now it seemed, it seemed almost violent and intrusive in the way its performed.

Casey thought back to earlier that day when they had arrived in the room that had been set up months ago for use of updating the Intersect and there had been a chair fastened securely to the floor. He could feel the hairs on the back of his neck raise at it wondering what exactly was going on. It wasn't until Chuck stepped near the computer in the center of the room in front of the chair and the techs had him sit down did he completely understand.

Sarah was the first to respond as the first tech reached down to secure Chucks arm to the chair. She grabbed hold of it and twisted it to his back. It didn't take much effort considering he was just a tech but her angry yell demanding what he was doing echoed through the room.

The tech stumbled through an explanation stating that with the data updates Chucks been going through that he'll close his eyes or collapse in the middle of it causing a break in information that could potentially be damaging to the information in his head as well as Chuck himself.

Chuck weakly, already exhausted from the mission from the previous night and the update only two days ago which still caused him head pains called Sarah off. Making a joke as he always did saying he could use a seat during these things, she let it go and watched the techs with a hawk eye as they strapped him to the chair and forced his eyes open.

Casey had to admit to himself that he didn't like it all. It looked like a medieval torture device and brought back memories of the Fulcrum cell in the suburbs. He stood in front of Chuck for several moments trying to read his reaction, telling himself that if Chuck gave him any indication that he was hesitant about this getup he would break the kid out of it and cancel the update.

He saw nothing however except an exhausted smile and a quiet reassurance that he was fine. With that Casey and Sarah walked out of the Intersect room and into the observation area to watch the update take place. He watched from the safety of that room with glasses to protect him as images raced across the computer screen and all around the room at a rapid pace.

He hated to admit it but the speed of the images around was beginning to make him feel slightly sick, but he didn't want to close his eyes. If Bartowski had to endure this torture, and on a regular basis now than so can he. At least that's what he thought and told himself until he heard the moan of pain coming from inside the room that rose as the process continued.

"Shut it off." Casey had shouted at a tech who shook visibly from fear of the large man.

"We can't. If we shut it off mid process it can cause irreparable damage to the host and the Intersect." He stuttered out, cowering slightly away.

Casey glanced at the download bar seeing the process was almost done. He readied himself to run into the room the second it was over and rip the restraints off of Chuck. The second the images stopped and the room went dark both Casey and Sarah were in the room before the lights came on.

What he saw scared him, and he wasn't an easy man to scare. Chuck eyes were moving rapidly back and forth as his body convulsed violently. Blood dripped out of his nose causing a stain to form on his shirt. Casey tried to gain his attention by calling his name and gently tapping his cheek, but the only sound that came from him was moans of pain as he began sliding out of the chair once he was released.

Casey immediately bent down to pick Chuck off the ground and he carried him to a room off to the side down the hall that had been set up for this as well. Sarah thought it was better to set up a room then leave Bartowski lying on the floor for the time he's passed out after each update.

Casey had laid him on the bed carefully and arranged him on his side in the event that he got sick, the convulsions seeming to have lessened in the transport but still visible. He was glad now that he had put the bucket by the bed.

That had been almost two hours ago.

Two hours Bartowski had been unconscious in the room with Casey hovering by the door and Sarah sitting by the bed stroking his hair. He hated to admit it, but he was beginning to worry.

"Should we try to wake him up?" Sarah asked concerned an hour after the vomiting incident. Chuck showed no signs of waking up on his own and it was beginning to unnerve them.

Casey shrugged, not sure what to do.

"Chuck, Chuck sweetie, you need to wake up now." Sarah said softly to him. She stroked his cheek in a loving way that if it was any other time would make Casey roll his eyes and grunt. Now however he watched like a hawk for any sign that he'll awaken. "Come on Chuck, you have to get up now so we can go home."

The man on the bed scrunched his eyes closed and turned his head away from Sarah. Casey met Sarah's concerned gaze and stepped towards the bed.

"Yo, Bartowski, get up!" He shouted, earning a glare from Sarah. Casey just shrugged her glare away, not feeling bad at all for yelling at the obviously ill man.

Chuck's eyes opened suddenly then, startling them both causing them to back away from him. After a moment of no movement they leaned over him to get a closer look. Casey noted that his eyes were glazed and unseeing and he wondered idly if Chuck was even awake or if it was some kind of reflex.

Chuck's eyes blinked closed slowly before rising again, his eyes coming more into focus. His hands balled into fists tightly before loosening. Casey looked over at Sarah as she watched his movements with alarm, unsure as well as to what was happening.

"Chuck, are you alright?" She asked him softly. Chucks head turned towards her and Casey watched as his mouth moved in a way as if testing its motion, trying to get words out. For a second Casey was worried about minor brain damage but scoffed it off , believing that the update had just been too intense for the kid.

"Are you ready to go home?" Sarah asked him. Casey rolled his eyes as she tenderly placed her hand on his face and began stroking it softly. Chucks eyes were directed towards her, staring unblinkingly, unnerving Casey.

They both waited several moments but no response came from Chuck. He continued to stare at Sarah with unblinking eyes and move his mouth as if to talk but no sound would come out. Casey had enough of that, and to be honest enough of this facility for the moment so with a grunt he bent forward to help Chuck up.

He was unsteady no his feet, his legs curling underneath him as if he had no bones. It took both Casey and Sarah on either side of him to help him stand up. Casey could have easily carried him but Sarah suggested that the short walk to the car would help get the blood pumping again and hopefully help Chuck come out of whatever was wrong with him.

With that they half dragged half carried Chuck down the hall. Casey noted that the technicians from the update were standing in the hallway watching with interest and taking notes on their clipboards and iPads. It unnerved him the interest they were taking and he thought that perhaps he should be more worried about what all these updates have been doing.

By the time they exited the facility Chuck seemed to have regained his ability to walk and took some of the weight off of his handlers. By the time they reached the car he was standing straight on his own looking around the place with wide eyed wonder.

They stood outside the car for several moments, Casey prayed that this was a sign that Chuck was feeling better and wouldn't be vomiting all over his car. Sarah stood by him as Casey walked to the other side and unlocked the doors.

"Get in Bartowski." He barked. Chuck didn't startle like he normal would. Instead his head just whipped towards Casey, staring at him with the same unnerving blank stare but without moving to enter the car. Casey wasn't sure what to do. He knew if Chuck was fine he would growl at him and bark some insult finished with a veiled threat he wouldn't actually carry out. However, with Chuck just getting this update and obviously not well, he wasn't quite sure what to do.

Luckily he didn't have to think about it too much longer as Sarah placed her hand on his shoulder and opened the door for him. Casey and Chuck continued their staring contest for a moment more before Sarah more forcefully pushed him into the back of the car.

Casey shared a look with Sarah before she herself got into the back with Chuck. Casey stayed outside for a moment, taking a few breaths and clearing any cobwebs that may have formed in the two or more hours he was stuck waiting for Chuck to wake up. He hoped he wasn't stuck babysitting a brain dead asset now.

He finally got into the vehicle and closed the door. He looked in the review mirror at the two in the back before turning the car on. He could see Walker had a tight hold on his hand but Chuck didn't notice as he was still looking around in wonder. It was odd to see and for a second Casey was curious on what Chuck was looking at or for. Curious on what he could be seeing that would cause such wonderment to appear on his face. What kind of update they gave him that would cause such amazement in him.

The ride home was mostly silent, the only sounds other then what came from the car was Sarah in the back, softly talking to him trying to get a response but so far no luck. He just continued to look around at the passing scenery as if he's never seen something like it before. Casey and Sarah kept passing worried glances to each other but didn't say anything, not wanting to alarm Chuck if he was in some way paying attention.

Once they arrived back at the apartment at Echo Park, Chuck got out of the vehicle after Casey opened his door and pulled him out. Standing straight up at his fullest height Chuck stood where he was and watched with unblinking eyes as Casey walked away, leaving Sarah to walk him home.

Not wanting to leave Sarah alone with whatever shell Chuck currently was he followed the two into Casa Bartowski and watched as Chuck stood at the door like a guest in his own home. He looked around the place like he'd never seen it, his look calculating as if looking for threats.

"Chuck, I think you should rest. You seem pretty out of it." Sarah told him gently. Again no response was forth coming as he stood there looking down to her, watching her every move.

She took charge then, grabbing onto his hand and entwining their fingers as she tugged gently down the hallway to their bedroom. Casey knew he should follow them, but stayed in the front room, not wanting to be party to whatever hanky panky takes place between his partners as they get ready for bed, but he waited in the living room, grabbing a tumbler and pouring himself a bit of scotch.

Twenty minutes later Sarah came walking out slowly down the hall, her face wary and concerned. Casey offered her a glass of her own but she declined it, wrapping her arms around herself concerned.

"That was really weird." Sarah stated first, breaking the silence that was stretching between them. Casey agreed. He spent tons of time telling the guy to shut up, but his silence at this time was unnerving.

"You think he's just out of it or something's wrong?" He asked her tipping the glass up to finish the scotch that was in it.

"I don't know. It was just , weird. I don't think Chucks ever been that quiet before. Even when he sleeps he's still talking or making noises."

"Ugh, Walker, more than I need to know." Casey ground out rolling his eyes. Sarah however wasn't buying it, knowing that he was just as concerned.

"You should already know that Casey you spent two years with surveillance in his room." She scolded him. But her annoyed expression turned to one of concern. "He was just like a robot. I told him what to do and he did it. Change his clothes, brush his teeth, lay in bed. I told him to close his eyes and he did it immediately."

"Yeah Bartowski doing as he's told is cause for alarm." Casey joked lightly, though neither laughed at it. "What do you think we should do about it?" Sarah looked at him alarmed that he would ask her to take point.

"Why are you asking me?" She asked, causing him to roll his eyes again.

"He's your boy toy Walker. Whatever we do or don't any damage he's taken you're the one who's going to have to deal with it until you dump his ass." He pointed out. Sarah huffed, not liking what he was saying. Casey felt momentarily guilty at the way he phrased it though it was the truth. Although he was pretty sure as much as he'd hate it and grumble about it, he wouldn't leave her alone to deal with the situation.

"I think for now we just let him rest and then we'll see how he is later. That update was brutal. They're getting worse." She said concerned sitting down at the dining room table. "I don't understand what they are updating that needs it so frequently. Intel can't have changed that much could it?" Casey shook his head.

"No, intel changes but if they did an update each time that happened it would be several times a day just to keep up. Maybe they'll doing some software updates or something." He suggested, pouring more scotch.

He watched as Sarah leaned on the table, placing her head in her hands as she thought about everything that was happening. He took note of how tired she was and how warn she seemed to be. She'd obviously been worried about Chuck for a while now, and the frequent missions hadn't helped much on the exhaustion and stress they had all been feeling lately.

"I'll leave you to it then." Casey murmured, rinsing his glass out and placing it on the counter. He walked past Sarah at the table and placed a comforting hand on her shoulder. "If there's any problems or you need help contact me." With that he gave her a final look before exiting the apartment, worry filling him.

The tech at the CIA facility watched out the window watching as the female agent, Sarah Walker opened the back door to the car they were driving and gently shoved him in. He hadn't taken his eyes off them the entire time they had walked through the place. Once they drove off he let out a giant grin as he rushed back to the phone on his desk.

He dialed the phone number he had memorized by order as to not leave any evidence lying around for others to find and waited for the other line to pick up.

"Well, how did the upgrade go Dr. Krinshaw" The voice on the other end asked.

"It went as planned Director. Carmichael was out for several hours and his handlers watched over him while he was out and wouldn't allow any of us to examine him. However when he came out he was supported by both of them and curiously he didn't seem to recognize anything." Dr. Krinshaw reported. There was silence on the other end as the Director listened and processed the information.

"What does that mean? Did the upgrade take?" He asked impatiently. The Tech shuddered slightly at the angry tone, feeling the wrath of his employer through the phone line.

"It's unclear at this moment Sir, but going just off visual observation it's possible that it wasn't Carmichael that was in control, it was the Intersect." He delivered excitedly. Again there was silence on the other end for a moment.

"What gave you that idea?" The Director inquired curiously.

"Well, the vacant expression on Carmichaels face, as well as the way he had to be dragged out but seemed to gain his strength and be fine by the time they hit the car. The Intersect is program to observe and learn. It learned how to stand and walk in the time that they exited the facility." He said, practically shaking with enthusiasm.

"Did his partners notice anything suspicious? We can't have them finding out before the final programing is uploaded into him." The Director stated harshly.

"They seemed concerned at his lack of coordination and silence but other than that I don't believe they suspect a thing. Most likely they're caulking it up to a hard update. It was very brutal." He admitted, grimacing at the remembrance of the expression and shouts of pain that came from the Intersect room during the process.

"Good. We shall proceed with the final stage in two weeks' time. That should give the program plenty of time to observe and assimilate human interactions into its programing." With that the Director hung up leaving the tech to look at his phone with a frown before hanging up.

Dr. Krinshaw sat back in his chair and thought for a moment, a grin appearing on his face. He had worked hard on the upgrade to the Intersect, and was delighted when the Director approved it to be put into effect. At first he had been hesitant when he was informed it was to be disguised as a regular update instead, not allowing him to inform Agent Carmichael what the update actually was.

He had moral qualms with it at first but after being given free reign and made head of the project the Technetium just through all morality out and let the excitement of the project take over. In a few more weeks he will have successfully been the first person to create and AI in a human Host. The program had just finished being installed into the Hosts mind and will start to take control. The only thing that was left, that needed to be done to assure complete cooperation from the Intersect was to get rid of Carmichael. In other words, to Wipe him from the Hosts mind so the Intersect had complete unobstructed control.

A/N: Yes another story already. I know I've spoiled you all with fast updates but I'm trying something new again so this story will hopefully have some action and technical stuff, things I'm not sure how to write so update will probably be slower. I haven't really written much action before so I'm looking forward to trying it.


	2. Chapter 2

A/N: YAY! I have me a Beta! Thank you charahkids!

Chapter 2

Confusion was the first thing that Chuck felt when he awoke the next morning. He opened his eyes slowly, blinking several times to adjust to the light filtering into his room before he was able to fully open them. The first thing he saw was his Tron poster, hanging on the wall like it had for many years. He stared at it for several minutes, letting his mind try to wonder on how he came to be in his room.

After several minutes he took a deep breath and turned onto his back, watching his room rotate with him as he turned. Everything looked the same as it did when he left it last time except the light from his window was definitely morning instead of midafternoon.

Chuck closed his eyes again and focused on breathing. After counting to ten he finally pieced together what he remembered starting with the afternoon, the last time he had been in his room, or their room. A small smile crossed his face at that correction, thinking of the room that had been his for over ten years as no longer just his but theirs, the room he shared with the one he loved.

Brining his mind back to focus, last he remembered he was getting dressed after an afternoon session of expressing love to Sarah. They were supposed to meet Casey in the courtyard in ten minutes to go to the CIA facility where he was to receive yet another update for the Intersect. They had been discussing asking Beckman for a small reprieve before the next update. He'd had five in the last two weeks and the intense violation of having data stored into his mind was beginning to take a toll on him physically and mentally as well as the stress on the team as they still had missions.

Sarah expressed her concern for his wellbeing and he agreed with her and had promised with one last passionate kiss before they exited the room that he would speak to Beckman as soon as he could about it.

The drive over to the facility had been silent for the most part, the beginnings of a migraine already starting to stretch through his entire head and down his neck. He tried not to show any pain and just smile at Sarah, holding her hand tightly in his. He was feeling tired, exhausted really. They had a late night mission that lasted into the early morning. Both Sarah and Chuck had come home, took a quick shower that involved much to his dismay just showering and crashed half hazard onto the bed.

By the time they got to the facility the migraine had been in full force and Chuck had a hard time even walking. He held tightly to Sarah noting the concern on her face and tried to smile at her to reassure her. He wasn't even paying attention to what went on around him until suddenly Sarah wasn't holding his hand and was instead assaulting a technician in front of him.

After a moment shock he pulled his wits about and called her off, telling her it was alright. The chair that sat in front of the Intersect computer did look quite frightening and memories from the mission in the suburbs came to mind. It took a lot of will power not to flinch away and fight back when they went to pry his eyes open, but he knew it was necessary. He was so tired and worn, the pain in his head already too great that he wasn't quite sure he would be able to keep his eyes open on his own anyways.

That was all he could remember until now. The lights went off; the screens came on and then nothing till now.

Chuck stared at the ceiling of the bedroom for another few moments, trying to see if he could assemble some kind of memory, even if it's fragmented on what happened between then and now. But there was nothing, his mind was completely blank.

He turned his head to the left, expecting to see Sarah there though not really surprised not to. Based off the suns position coming in his room he'd say it was mid-morning and Sarah while not really a morning person would be up by now checking reports or doing a workout. He laid there for several minutes before finally pulling the blankets off him and sitting up.

His head spun as he sat at the side of his bed causing his eyes to close tightly. He felt bile rise in his throat and he tensed himself to force himself not to throw up. He wondered idly if perhaps his lack of memory had anything to do with drinking the previous night. He knew that Morgan was getting kind of that he and Chuck haven't been able to hang out much recently, and drinking would be something he would agree to if it made his little buddy happy. However remembering the update and the migraine before he doubted that was it.

After a few moments he was finally able to feel himself stabilize and he opened his eyes slowly once again to look around. He noticed his glass of water he typically had on his bedside table for bed sitting there and he reached out and grabbed. He hungrily drank the water down, reveling in the cool liquid as it slid down his throat. He drank the whole thing down, coughing as he finished it from drinking too fast. He set the glass down on the nightstand again and covered his mouth and tried to quail the coughs.

At last they settled down Chuck took one final moment before finally trying to stand. He felt unsteady on his feet but still placed one foot in front of the other till he was using his arm to lean against the side of the door. He took the second there to look down at his What's this about Sarah?s, noting he was in his pajama bottoms and a sleep shirt. He couldn't remember changing his clothe, but they were on straight enough that he figured he must have put them on.

His feet feeling steady he opened the door slowly and walked out. He could smell coffee coming from the kitchen and walked in that direction, letting it lead him. He was never really any good unless he had at least one cup of coffee. Chuck was always ashamed that he had become one of 'them'. Them being the people of the world dependent on a morning dose of caffeine to get started, but with his odd shifts and jobs in the past three years he's needed that boost in the morning.

Reaching into the cupboard once he reached the kitchen he immediately poured himself a large cup, bringing it up to just under his nose. He smiled at the cup as whatever nausea and cobwebs he felt washed away with the delicious smell of the bitter coffee. Taking a sip he took that opportunity to search his memory again only to come up blank.

"Good morning Chuck." Sarah said startling him as she came up behind him wrapping her arms around his waist. He jumped slightly but thankfully didn't spill any of his precious coffee on the counter or worst, himself.

He set the coffee cup down, albeit a little reluctantly and turned around in her arms and smiled at her. Hunching down slightly he captured her lips with his and gave her a soft kiss, wrapping his own arms around her. Pulling back a few seconds later he stared down at her with a grin on his face.

"Good morning to you Sarah." He said lovingly. She stepped up on her toes to place a couple kisses on his jaw before pulling back slightly, he felt a shiver run from the spots where her lips touched him down through his body.

"Are you feeling any better today?" She asked him. He felt a loss against him as she lowered her arms and grabbed his coffee from behind him. He wanted to hold her longer but instead followed her, with his coffee into the living room.

Sarah stood in front of the couch waiting for him to catch up and for him to sit first before handing his cup back to him and sitting down next to him. He wrapped his arm around her shoulder as she snuggled into his side. He took another drink of his coffee as he relaxed into the couch and enjoyed the moment.

"Well, are you?" Sarah pressed a few minutes later, breaking the silence.

"I'm fine Sarah. Healthy as a horse. Whatever that means." He joked giving her another smile. He placed a tender kiss on her crown and looked down at her.

"I'm glad. That update was rather brutal. You were so sick." She commented embracing him, burying her face into his chest.

"Well the good news is I don't remember a thing, so there's that." He joked. He felt Sarah's eye narrow in his chest before she pulled back to look at him confused. "What?"

"Nothing at all?" She asked him confused. Chuck thought one last time, his mind zooming back through all the memories of yesterday. Nothing stuck after the update started.

"Not a thing Sarah. What's wrong?" He asked her feeling slightly alarmed. He was prone to worry so the feeling is not foreign to him, however seeing worry appear on Sarah's face always brought it up a notch being as she's a superspy trained to hide her emotions.

"It's just, nothing? At all? you don't remember the ride back or getting ready for bed or anything?" She asked him searchingly pulling back further from him.

"I swear last thing I remember is the update starting. How did we get home? Did Casey carry me?" He asked her feeling dread in his stomach. If Casey carried him home and had to help him get ready for bed he would never hear the end of it. The man held grudges like no one else in the world Chuck knew.

Sarah didn't answer him, instead her eyes looked over his shoulder slightly glazed as in thought. He wanted to press her more about what was wrong but he'd learned long ago that pressing Sarah for information was useless. He would just have to wait and wonder until she was ready to give information freely.

"After the other updates, did you miss any time?" She asked him after a while. Chuck thought for a moment, back to those updates. All he could remember was pain afterwords and lying securely in Sarah's arms as the dizziness passed after he woke up. Aside from the time the update started and waking up then he didn't think he missed anything.

"Not that I know of. What's this about Sarah? You're starting to freak me out." He admitted to her. He watched her intently as she went through some internal struggle for several minutes before she finally looked up to him and gave her best megawatt smile. Normally anything and everything would disappear from his mind when she gave him that smile but he felt some sort of foreboding.

"It's nothing Chuck. Don't worry about it." She told him, kissing him. He was about to protest but as always kissing Sarah filled him mind with rose petals and music, disrupting any other thought from creeping into his head. "We better go, Beckman wants a briefing." She said pulling away from him causing him to groan.

"Can't we just blow her off and stay here? I feel sick." He said giving her the puppy dog pout he could, but her alarmed look at that wiped it right off his face.

"You said you were fine. Are you sick? What's wrong?" She asked alarmed pressing her warm hands onto his face. He loved the feel of them, but he grabbed them from him and brought her palm to his lips placing a kiss on it.

"I am fine, I'm joking. I just want to stay here with you." He told her lovingly, brushing back some of her hair from her face. Her expression flickered from concerned to annoyed then finally on impassive in a blink of an eye. He made a silent note to himself not to play sick anytime soon.

"That's not funny Chuck. Now go get dressed." She said firmly standing up and away from him. He wanted nothing more than to pull her down back on the couch with him to snuggle more but the determined look on her face prevented him.

With a final sigh he drained the remaining coffee from his cup and stood up to go back to his bedroom to get ready.

The ride to Castle was silent. Once he was showered and dressed Chuck came back out to the living room to see Sarah standing in practically the same spot he had left her, though this time her phone was in her hand and she seemed to be texting.

He grabbed his keys from the bowl by the door but Sarah quickly took them away stating in a tone that left no room for argument that she would be driving and walked out the door and waited for Chuck to follow before quickly closing and locking it.

That was the last words she said to him as they got in her Porsche and started driving towards Castle. He wasn't quite sure what he did wrong, if he did anything wrong. He spent the trip reviewing everything that they had talked about, everything going fine until he made the joke about being sick. Obviously she didn't like that and he wasn't sure why she took it so personally.

He opened his mouth several times to try to say something but nothing came out as they zoomed down the street. She turned hard cutting off another car causing Chuck to grab hold of the door as she barreled through the intersection and into the parking lot of the plaza where the Buy More sat and parked the car.

They sat there for several moments, Chuck trying to get his breath back as Sarah stopped the car and took off her seat belt. They sat in silence for several moments lost in their own thoughts.

"Sarah I-"

"It's fine Chuck." She said cutting him off. He frowned for a second before turning his body, best he could to face her.

"It's not fine when you're mad at me." He told her earnestly. Sarah gave him a sad smile back before turning to look out her window for a second.

"I'm not mad at you Chuck. I'm just concerned. "She admitted.

"About what Sarah?" He asked but got no response. "Sarah, please, talk to me. I know you don't like to but we have to talk about you know, stuff otherwise we get into trouble." She looked at him then eyes narrowed in confusion.

"What do you mean trouble?" She questioned causing Chuck to give a patient sigh.

This was always the hardest part of their relationship he felt, but he was always determined to do it. Chuck had grown up with Ellie raising him, Ellie being an emotional person to begin with and taught him it's better to talk about ones feelings then letting them fester, or something like that.

It had started soon after their mom had left them and Chuck was having a hard time dealing with it. He had changed and become more secretive and quiet, not wanting to put more pressure on her or their father from the stress they already had. It had gone on for several months until Ellie got ahold of Chuck's report card and saw his grades slipping.

"We can't do this Chuck. If you need help or having trouble with things you have to tell me." She had pleaded with him that same afternoon. Chuck had felt guilty that he had let it get so bad.

"I just don't want to be a burden." He told her sadly, curled up in a corner of his bed. She had wrapped her arms tightly around him embracing him. He felt warm and safe, the safest he felt since their mother had left.

"Chuck, you are not nor will you ever be. At least not to me. But we have to fight against out nature and talk about things. We have to be a team, and that means no keeping secrets, reaching out when the other needs help. I don't know what I'm doing. I'm just a kid too." She had pleaded with him. And he took it to heart. Since then up until the Intersect came into his life Ellie had been his confidant and he always told her everything.

Dating Sarah, loving her was the complete opposite of how he was raise. She was taught to keep her feelings to herself, not to talk about anything. Keep face that everything was fine. Communication was not her strongest point and he knew that going in, and he loves her despite that.

"What do you mean trouble?" Her voice echoed bringing him back into the present.

"I mean, like, communication wise. We let the unsaid fester and then it gets blown out of proportion." He said desperately, not wanting her to be any angrier with him. "You say you aren't mad at me but your actions state you are, and I just don't understand or know what to do." He admitted.

He watched as her features softened from annoyed confusion to understanding and love. She reached her hand out to him and Chuck held on tightly to it like a lifeline.

"I'm not mad at you Chuck, I promise. I'm just, really concerned." She told him. He heart slowed down from the pounding he hadn't realized it was doing in anxiety. He was relieved to hear that.

"What's there to be concerned about Sarah? I'm fine." He reassured her, holding his hand to his chest. He gave her his best grin trying to settle any insecurity she may be having, but she just shook her head.

"No you're not Chuck. These updates are…" She didn't finish and he knew what she was trying to say. They were hard and violent. Nobody knew that better then him.

"I know Sarah. But there's only one more of this set. After we'll just have to be more firm with the General about them. That they need to be further apart. Ok?" He told her softly. She nodded her agreement before leaning over the middle and kissing him. Chuck pressed into her best he could in the small car, wanting to get as close as possible to her, forgetting that they were in the middle of the plaza barking lot. He was starting to really get into it, running his fingers into her hair when a loud knock at the window on her side startled them both apart.

They jumped apart slightly, both out of breath as they looked over to the driver's side window to see Casey standing there in his Buy More green polo shirt with a grimace.

"Are you going to attend the ing or are you just going to do the horizontal mambo in public?" He growled out. Sarah nodded her understand and he walked off with a roll of his eyes.

They took a second to get their breath back before finally making eye contact. The disarray of their clothes and hair caused them both to laugh, breaking the passion that had been permeating the air. They took a moment to fix themselves up before finally exiting the car and entering the Orange Orange to get into Castle.

Director Jordan of the CIA read the report he had been sent by Dr. Krinshaw once again. He was excited by this latest development and couldn't wait to test it out. If it worked it would be a huge step for the US intelligence community.

He thought again for the hundredth time if perhaps he should share this information with General Diane Beckman. It had been determined that while it is a joint NSA/CIA operation the little NSA General would take point and tend to whatever was needed.

Director Jordan did not like that.

Sure he got daily reports of the activities of the team but he felt like he was out of the loop on it and all attempts to get into the inner fold had been shot down with the Joint Chiefs, citing that the Intersect was precarious and didn't trust other government officials easily. Considering the instability of it, they were worried that any change could cause the Intersect to stop working.

Director Jordan grinned thinking about that, reading his report. With this latest upgrade it would no longer be an issue. They will have their Intersect and it will work perfect without any pesky human emotions or whatever issues Bartowski had that would stop it from working properly.

He had informed General Beckman it was just an update, a large one needing to be done in a series of six steps. He wondered if perhaps he should tell her of the upgrade instead but decided against it. She'll be pleased with the results soon enough.

A/N: Dude, so sorry it's taken so long. I caught this nasty cold bug so all I've done since Monday is lay in bed and watch my new Chuck blurays. you should have seen my hair this morning, dude, note to self: Just because you're sick doesn't mean you don't brush your hair. *facepalm*


	3. Chapter 3

A/N: Thank you to my beta charahkids! and thank you to the couple of you that reviewed! I really appreciate it!

Chapter 3

Apprehension filled Sarah as they pulled up to the building they were to check out for a supposed terrorist sleeper cell. She wasn't sure going on a mission right now was the right course of action but between Chuck's babbling of he was fine and neither Casey nor Sarah speaking up about the real reason they didn't believe this was a good idea, the General finally vetoed their request to palm this mission off to another team.

She had argued with Casey afterword's as they readied for it about the practicality of taking this one when there was an unknown happening to Chuck. He agreed with her, of course he did, but it was him that initially stated, though she fully agreed that for now they shouldn't tell the General about Chuck's black out.

So here they were sitting in the van outside the building putting on their final armor and double checking their weapons before they go in and see what's inside.

Sarah watched Chuck carefully as he checked his tranq guns and double check his pouches in his vest to make sure he had backups. She had wanted desperately to talk to him about it but she didn't want to freak him out or worry him. She prayed that it was a decision she wouldn't soon regret.

"Alright, everyone ready?" Casey asked as he slammed the mag into his gun making a loud click. Typically Sarah loved the sound of that, making her feel secure and ready for anything but tonight it just caused her to jump slightly. Casey glanced at her pointing his head slightly in Chuck's direction.

"I'm good to go. Chuck?" She said walking up to him. He smiled at her as he fastened down a pouch and leaned down to place a gentle kiss on her lips, causing her to smile as well. They turned towards Casey as he groaned in disgust causing Chuck's grin to get bigger.

"What's the matter big guy? Want a good luck kiss as well? Come here." Chuck opened his arms wide and walked towards Casey. He growled at Chuck and smacked him hard in the chest causing him to let out a yelp.

"Can it Moron. You want to let them on that we're here already?" He hissed looking around. Chuck just walked back towards Sarah and the van, closing it the doors.

"Walker you take the Northside, Bartowski the Southside and I'll go in the second floor window on the west side. Got it?" Casey instructed them. They nodded their agreement and they all ducked low to the ground and went to their side.

Sarah took a few breaths before she entered through the Northside. Glancing in a nearby window everything was pitch black and left over furniture from whenever the building was last use for legitimate business littered the room. The window was cracked and falling off to which she was grateful for.

Carefully she knocked a few pieces of glass out, cringing and pausing for a moment as it hit the floor on the inside. She waited to see if anybody would come to investigate but nobody did. After making a large enough hole she was able to get her hand into the window in order to hit the lock on the side. She was pretty sure she could have just forced the window open, the lock being as old as it was but she didn't want to risk making any more noise than what was necessary.

Slowly she opened the window and crawled in. She landed softly on the floor below, dust flying up surrounding her. She held her breath for a moment to avoid breathing any of it in before finally looking around. The room she was in hadn't been used in years.

Creeping across the room, careful of any loose floor boards that could squeak and possibly give her position away, she walked to the door that was closed and paused on the side listening for any noise coming through. Hearing none she opened it slowly looking out into the empty hallway.

"Anything yet?" Casey's voice echoed quietly in her ear. She waited for Chuck's response of 'negative' before responding.

"I'm about to enter the hall on the north side. Everything is dark, no sign of life." She said softly opening the door further.

She crouched to the ground, hiding in the darker shadows there as she walked sideways along the hall. As she got to the end she peered around the corner near a staircase. She saw just beyond it a closed door with a light on underneath.

"Targets on the first floor near the staircase on the Southside." She said into her mic.

"Affirmative." Chuck's voice rang in. She looked across the way and was able to see him standing just above the rail of the staircase. He gave her thumbs up indicating he saw her too.

"Second floor clear, making my way down." Casey responded. They waited in the shadows for him to come down. The silence was beginning to chill her, not able to hear any noise coming from the room beyond.

"The silence is kind of eerie." Chuck said, causing a smile to grow on her face as if he read her thoughts.

"Chuck, do you hear anything from the room?" She asked in the mic. She watched as Chuck crept closer to the closed door for a second before moving back.

"Nothing. Anyone else creeped out?"

Before Sarah could respond however a distinctive click echoed behind her and she felt the barrel of a gun poke her in the back of the head.

"Move forward." A male's voice said. "And drop your weapon." Sarah complied, lowering her gun to the floor and raising her hands in the air. She looked across at Chuck seeing him in a similar stated.

"You're good, I didn't even hear you." She said as she stepped into the entry way next to Chuck. Her world tilted dizzily and pain erupted in her head from the butt of the gun coming down on her head. She heard Chuck yell as she went down.

She felt hands grab tightly on her shoulders to bring her back up. Shaking her head to clear the remaining confusion she drew her elbow back and popped it into the man's mouth that stood behind her. Quickly she grabbed his arm pulling it behind him and smashing her foot into the back of his knee causing him to collapse.

The man dropped heavily on the floor in front of her moaning out loud in pain as she turned to take care of any other assailant to find the other one dropped on the ground next to the other, Chuck standing next to her panting.

She smiled at him happy they had taken them down with minimal effort only to have it fall from her face as she looked at Chuck in the dark.

His stance was still ready for a fight but his eyes fluttered back and forth as if flashing. More perspiration than normal covered his face as he appeared to be struggling.

"Chuck?" She asked alarmed. She rushed to him placing a hand on his cheek feeling it burn. She was so focused on Chuck that when the lights in the entry way turned on, chasing away the darkened shadows she jumped, startled.

Looking around she was surrounded by guns. By her estimate there were about twenty men there, heavily armed, more than they estimated would be in this cell. Her heart beat faster as the situation quickly escalated out of control.

A man stepped forward from behind everyone else, exiting the room to the left that had the light underneath. Sarah felt a chill down her spine as the man before her eyed her up and down, probably having disgusting thoughts about her. It was obvious by the way the others acted that he was in charge.

She glanced at Chuck, hoping to see if maybe he might have some kind of plan to convey to her only to be faced with him hunched at the shoulders and hands tightly tangled into his hair pressing his head. His eyes still fluttered wildly and his face was pinched as if in pain.

"Casey?" She said softly hoping it was loud enough to be picked up on the com but not loud enough to alert those around him.

"Yeah, I'm here." He said gruffly coming down the stairs. His hands were raised and he had a look of annoyance on his face. Four or five more men with weapons followed him down until he was standing next to her. She watched him as he glance at Chuck then shared a look with her, his look of calm indifference replaced by one of concern.

"What are you doing here?" The man stated harshly looking between Casey and Sarah obviously finding Chuck to be no threat. Neither of them answered as they glared angrily at him. "Who do you work for?"

Again nothing. The man pulled out his gun and held it in his hand, pointing it at the ground as he scowled at the agents in front of him. He paced in front of them for a moment and Sarah took that time to prepare herself for the fight she knew was coming. Glancing around at all the men around her she didn't know if they would be able to get out of this situation alive, but she wasn't going to just stand around and let them kill her. She was going to fight tooth and nail, and she was going to do everything she could to protect Chuck.

She quickly glimpsed at Chuck next to her again concern filling her still for his wellbeing. Something was happening to him and she didn't know what and she couldn't find out while surrounded. He looked like he was stuck in a flash and it worried her.

Though he refused to use deadly force she was more than aware at how deadly Chuck could be, how much of an asset he is in a fight when it comes down to it. However he was most vulnerable while flashing as he was momentarily defenseless as it took place.

"I'm going to ask you one more time before I kill you. Who are you?" he growled out angrily. Sarah counted the seconds in her head, not taking her eyes off the gun in the man's hand. The situation was dire and Sarah wasn't sure how to get out of it. There were too many enemies with weapons around and there was no way they would be able to get out of it.

The man apparently lost his last bit of patience as raised his gun and pointed it at Sarah. He paused in that position giving her one last chance to answer. Sarah stared him down, hiding away any fear she was actually feeling. She could see his finger twitch in order to kill her. She wanted to close her eyes but refused too, if she was going to die now she was going to do so with as much dignity as possible.

A groan of pain caused both of them to jump slightly, the tension between the two breaking as they looked over to Chuck who had lowered his hands to his side and stared at the man who was about to kill her. Before she could even process a thought Chuck jumped at the man, causing his gun to drop and swung him around before placing his arm around his neck and snapping it.

Sarah stared at the man stunned as his body limply fell to the floor with a loud thud from Chuck's arms. Nobody said a word as they watched in horror as their leader died.

"Chuck." Sarah said softly, not quite sure what to say. Before she had a moment to gather her thoughts however Chuck grabbed the tranq guns from behind him and quickly pulled the triggers in rapid succession.

Once the darts were gone he threw the empty gun behind him hitting a man that had begun approaching. He grabbed hold on his arm and flung him over barreling into his comrades in front of him. A man ran up to chuck arm back fist clenched throwing as much weight into the punch as possible. Chuck easily grabbed hold of him breaking his arm and head butting him knocking him out.

He reached down and grabbed the gun that his latest victim had dropped and pointed it straight at the next person in front of him and shot him, kill shot to the chest. In rapid succession again he fired the gun unflinchingly to those around him until the magazine was empty.

Sarah watched in horror at everything that was going on around her. It was pure chaos and as she stood there dumbfounded. She was about to step over the body that lay in front of her when Casey grabbed her around the shoulders and pushed her to the ground.

"We have to stop him." She said desperately as Casey covered her. She struggled to get out from underneath him but he placed all his weight on top of her preventing her from moving.

"I don't think we can yet." He shouted over the sound of guns going off all around her. She closed her eyes tightly praying it would end soon. Her instinct was to get up and fight, to protect Chuck, to help Chuck, but she couldn't move with the weight of Casey on top of her.

Finally after what felt like forever the sounds of guns going off ceased and all was silent except for the quick breathing of both her and Casey. She felt Casey pause for a second and then lift his head to survey the damage before he got off her and let her sit up.

Her mouth dropped opened in shock and confusion. The room around her was darkened slightly from some of the lights being shot down but there was enough light to see the disaster that surrounded her. All around her lay bodies, some tranq some dead. Blood spilled and splattered across the room soaking everything in a horrid shade of red telling all who see it that something horrible had taken place here.

Her body shook as blood drained from her face and she shakily stood up on her feet. Looking up from the floor finally there stood Chuck, standing calmly in the middle, guns dropped lying at his feet. She took in his calm appearance and his blank stare. Her mind thought back a few minutes before this all happened, when he was stuck in a flash, pain written across his face. It was a different look from the look of indifference that he showed now.

Sarah stepped forward slowly, stepping over the bodies as she made her way over to him. His eyes were glazed and staring at nothing as she approached him, not seeming to notice her until she was right in front of him.

"Are you ok Sarah?" He asked mechanically finally looking at her. Sarah didn't see the expressive eyes she normally saw when looking into them. She didn't see anything at all, and the fear she had been feeling when it all started coursed through her.

She took a few stuttering breaths to calm her racing heart and glanced in Casey's direction for a moment. It frightened her further to see his stoic façade dropped as he looked around in horror at the destruction around them.

"I'm fine Chuck. How are you?" she asked him cautiously. His eyes glazed over for a second before focusing back on her.

"Chuck is fine." He replied.

Casey watched as the last of the bodies were carried out on gurneys and into the awaiting vehicle. All in all the final count was twenty nine.

Twenty nine bad guys. All taken out by Chuck Bartowski.

Casey shook his head at that unbelievable thought. He wasn't exactly sure how it happened, and if he could he wished he could imagine that it didn't, but somehow that nerd had taken out all those guys with guns and he didn't even have a scratch on him.

Casey looked over to their van towards Chuck. The doors were opened and Chuck sat on the bumper in the back with Sarah hovering over him. He looked empty and hollow from Casey's point of view as he sat there, back straight eyes ahead unblinkingly.

"Take those ones to the CIA detention facility for questioning." Casey barked out as he passed a truck caring ten of the men. The lucky ten. The ones who were fortunate enough to be shot with a tranq gun instead of a bullet.

He watched as the trucks back doors were closed and locked before driving off. He sighed deeply feeling tired all of a sudden. It always amazed him on how difficult this assignment actually turned out to be at times.

At first he thought it was a punishment assignment. Watch out for the nerd that ended up with all their secrets locked in his head. It was a babysitting job and he made it no secret how much he despised it. But then Chuck surprised him, over and over again during missions. Not only on his bravery to do what's right and protect the greater good, the exact reason he signed up for that job. But his integrity and ingenuity.

He would never admit it but despite all the screw ups, mishaps and his lame ass cover job, the kid had grown on him. No matter how far Casey pushed him away he was like a sad puppy always coming back, always trying to be his friend. And again he would never admit it even under duress of torture, but he appreciated it, being as he doesn't really have any people he would consider 'friends'.

It didn't hurt that his sister was an excellent cook and had a tendency to take in strays and feed them.

Walking across the parking lot away from the chaos of the NSA cleanup crew he had called in he approached the van. Sarah looked up at him immediately; her arms crossed over her chest her impassive expression back on. She looked slightly calmer then she did before when she had led Chuck out of the building through the front door.

"What happened?" he asked, wanting to roll his eyes at his own dumb question. He knew what happened, but he needed to hear it. Perhaps then it would make more sense to him and less like a nightmare come to life.

They both stared at Chuck then, expecting him to start stuttering or animatedly explain what had happened. But he continued to stare off in the distance at some unknown spot. The three of them stared in silence for several minutes none knowing what exactly to say. Casey widened his eyes at Sarah as she glanced at him indicating that she should prompt him. She bit her lip in her nervous way before reaching her hand out to his shoulder.

"Chuck, what happened in there?" She asked him, her voice calm and quiet. Chuck stared for a few seconds before his eyes blinked a couple times as he looked around.

"The man with the gun was going to shoot you." He said plainly, as if that would explain everything. They waited a few more moments before prompting him further.

"We know that numbnuts but what happened? You went all gung-ho in there." Casey stated annoyed.

"The man was going to shoot Sarah." He repeated mechanically. "Chuck couldn't let that happen." Anger rose in Casey at his non-answer and he had to resist the urge to strangle his partner. Sarah gave him a look that explicitly said to calm down and he tried to calm himself before speaking again.

"I got that Bartowski but did you have to kill them all?" He inquired.

"I did not. Ten men were left alive." Chuck said. Casey's eyes narrowed wondering how he knew that. Only he had been told the number and only because he was in charge of directing the cleanup. He decided to try a different tactic.

"Why did you kill them instead of knocking them out?" Casey asked Chuck. Chuck was silent for several moments' eyes once again glazing over for the moment.

"It is procedure when surrounded by enemies of more than three to one and you are unarmed with no back up contingency plan to take down as many as possible as quickly as possible." He stated mechanically. Casey looked at Sarah who's own eyes were narrowed, further alarmed.

"Chuck, you killed nineteen men." Sarah cried out, her voice quivered slightly.

"It had to be done."

"No it didn't. What is wrong with you? Are you in shock or something?" She shouted at him. Casey placed his hand on her arm to back her up a bit and she shrugged it off and stood right in front of Chuck who looked up directly into her eyes. "Answer me Chuck." She demanded.

"Chuck is fine." He said simply. Casey growled and pushed Sarah slightly to the side to take her place in front of Chuck.

"That's the third time you referred to yourself in the third person. Are you brain damaged? Did those updates finally make you crack?" He shouted. He was surprised when Chuck didn't look away or cower. Instead he looked directly at Casey.

"No cranial damage has been detected. All systems are functional." He replied. Casey growled and raised his hand about to back hand him when Sarah grabbed it and pulled him back like he knew she would. She pulled him several feet away from Chuck and stood with her back to the van.

"I'm going to kick his ass." Casey stated the second they stopped, looking back at the man in question.

"Something's wrong Casey." Sarah said plaintively. Casey bit back his 'no shit' retort. "Something's off. I don't know what but, Casey he killed."

"I know."

"And not just one person. He killed nineteen and he's acting like he did nothing and its all protocol." She said. "That's not Chuck. You know him, he wouldn't harm anyone. He won't even carry a real gun, but now he'll shoot to kill? It doesn't make sense."

"Since when did the kid care about protocol? He's always the first to break it." Casey muttered remembering all the times they broke rules and orders, mostly initiated by Chuck Bartowski himself.

"It has to be these updates. They have to be doing something to his mind." She contemplated. "The black out yesterday and now this, something is not right here."

"I hope he's not going to keep talking about himself in the third person. That is going to get old really fas…what?" he stopped mid-sentence noticing Sarah's eyes widening and look of horror crossed her face. She didn't reply as she quickly turned back around and walked quickly back to the van, Casey trailing after her.

She stood in front of him again anxiously biting the bottom of her lip again. Casey knew she was nervous about something but he didn't know what. Somehow she had made a connection that he hadn't and he wanted to know what it was. He didn't like being in the dark.

"Where is Chuck?" She asked him. Casey peered at her confused and surprised as he looked at Chuck and waited for Chuck's answer.

"He is not here. Chuck is fine." He responded. Sharing an alarmed look with Sarah he asked the next question, wishing immediately after that he hadn't.

"Who are you?" He asked. The man in front of him look straight through him.

"I am Intersect 3.0."

A/N: I so think i got in over my head on this one. I'm just not feelin it. But i will trump through to the end! Please RR if you wish. It makes me feel warm and fuzzy.


	4. Chapter 4

Disclaimer: I have no idea if any of this is possible. Its made up for the sake of this story.

A/N: I'm sorry I should have put a timeline so you know where it takes place. Its post S3. ignoring Chuck quitting the CIA and such.

Thank you to charahkids for betaing this thing. And thank you to all my wonderful reviewers. I have no idea where the hell this thing is going but your encouragement makes me keep pressing on.

Chapter 4

General Beckman was mad. No that was an understatement. General Beckman was pissed off, at many people. She was having trouble pinpointing the exact person to hone her anger on with so many people adding to her fire, but for now she was going to settle for the closest person to her, Director Jordan of the CIA.

She stormed down the hallway quickly with her many aides following at a brisk pace to keep up with her as she headed towards Director Jordan's office at the CIA building. Beckman buy passed his secretary, not even sparing a glance as she opened the door to his office and storming in, finally coming to a stop in front of the director's desk.

"Diane, what-"

"What do you think you are doing?" She bit out harshly. The Director gave her a smile and sat forward leaning on his desk with an impassive look on his face.

"What do you mean?" He asked curiously.

"Don't play games with me Jordan. What did you do to Chuck Bartowski?" She demanded slamming her tiny fist down on the desk. Director Jordan smiles a placating smile as he stood up and walked around the desk, motioning for all the people milling around his office to leave. Beckman's aids looked to her waiting for her nod before reluctantly exiting the door.

Beckman watched with narrowed eyes as Jordan closed the door and stood there a moment before turning back to her again, the same smarmy smile plastered on his face. Beckman crossed her arms over her chest and waited for him to speak, ignoring his gesture for her to take a seat as he rounded his desk once more.

"I assure you General, the Intersect is just fine. Better in fact." He said, his smile getting larger, making Beckman feel ill at ease.

"What have you done?" She said again, her voice low and deadly. The smile wiped immediately off Director Jordan's face and he leaned back in his chair sighing warily.

"I haven't done anything Diane. The Intersect was due for an upgrade and it was authorized. The joint chiefs approved of it."

"Why wasn't I informed of this upgrade to 3.0? Why wasn't Agent Bartowski made aware of this?" She demanded angrily.

"It was need to know and you didn't need to know." He stated firmly. General Beckman was seeing red at this point. Angry that she had been kept out of the loop in regards to this.

"Do you know what you've done? The Intersect has taken over Chuck. He killed nineteen men in a matter of minutes. He is dangerous and out of control."

"That's just it though General Beckman. He is not out of control. Not anymore. The Intersect was always a dangerous tool. We all knew that at the beginning, but now he's more in our control than he's ever been."

"But at what expense? At what price?" She argued furiously.

"At the price of one human Diane. Only one. The one that could save hundreds of thousands. The Intersect is a truly beautiful invention, and with the final upgrade-"

"If you think I'm going to let Bartowski go through that last upgrade you're out of your mind. I will take this to the President if I have to." Beckman threatened. Director Jordan's' smile returned at her threat.

"This upgrade was authorized by the Joint Chiefs Beckman." He stated. "Besides it's too late, the Intersect 3.0 is already completely upgraded and inside him. The final one was just a little, well, house cleaning."

General Beckman ground her teeth together to stop herself from biting out the words she wanted to say. As much as she was pissed off and as much as she disliked Director Jordan he was currently the head of the CIA and she had to play nice, at least for now.

"And what exactly does this Intersect 3.0 do?" She finally asked after silence stretched over them. The grin the Director gave her made her stomach curl and was afraid of his answer.

"It does everything that Agent Bartowski doesn't do." He said simply and sat back in his chair.

Sarah paced back and forth in front of the counter of the Orange Orange. Once they were done and everything was cleaned up and taken care of at the crime scene they had decided it would be best to come back to Castle and report to General Beckman what happened. Everything that happened, including the black out from the previous day.

To say that Beckman was pissed off at them would be putting it mildly. Sarah was pretty sure it wasn't about what happened tonight but about not telling her about what happened after the update the day before.

They had brought Chuck down to Castle and sat him down in front of the screen. Once the General had come on however he immediately stood up at attention, arms behind his back. Even Casey was impressed through his concern.

The General had ordered Chuck be locked down in Castle until she could get to the bottom of it and find out what exactly was going on. That had been hours ago and Sarah couldn't take just sitting there next to a stoic Chuck any longer. She had told Casey that she was going for a walk and had gone upstairs to the Orange Orange.

She didn't like this at all. She didn't know what was going on and she was scared, something she hated feeling. The unknown of what was happening to her Chuck scared her to death and she wasn't quite sure what to do about it.

The cold impassiveness in his eyes as they questioned him at the house and later in Castle caused a chill to run down her spine. She had never seen anything other than pure emotion from his expressive eyes. His mechanical way of talking and logic over what he had done had frightened her. Her Chuck was the sweetest gentlest soul she's ever met. He was a trained Agent now and still doesn't use a gun.

The only time she'd ever seen him shoot anybody was Daniel Shaw in Paris. She had been scared out of her mind unable to move, to talk, to do anything as the drug she had been given paralyzed her. She had watched in horror as Chuck tried to fight Shaw only to fail and unable to flash as he collapsed on the ground next to her chair in a heap.

Shaw had taken her to a bridge nearby, one she had walked on many times during her missions in Paris but this time it took on a dark undertone. She was well aware that he was going to kill her by throwing her over, letting her drown as her body refused to move to save her. It has been a fear she'd never shared with anyone, the fear of drowning and she was so close to it then.

But then her savior came and saved her from a horrible death. She watched through heavy lidded eyes as Chuck gave Shaw one last chance to surrender before finally placing three shots into his chest, causing him to fall backwards and over the bridge, almost taking her with him.

The last thing she remembered was Chuck arms around her and his soft voice telling her she was ok before she gave into the paralysis and her mind went to sleep.

All anyone knew after that was that she and Chuck had finally gotten together. She had stopped hiding behind her job and her walls she had built up and let him in. They had run away together planning on leaving the spy life behind and just be with each other.

What nobody knew about was the trauma Chuck went through afterwords. The nightmares he had for months on end. The depression he faced during quiet moments when he was lost in thought. She had swallowed her own feelings and tried to get him to open up to her during their journey but he had declined, which surprised her. He had begged her to just let it be and let him sort it out on his own first.

She didn't admit it then but that scared her too. The guy she fell in love with who was an open book and always shared his feelings and wanted to talk about everything to death and clammed to her about it. About how he was feeling about the nightmares he was having. About anything.

They did eventually after they got home, after he said goodbye to Ellie, after she agreed to finally move in with him and Morgan.

But that was then and this is now. He killed Shaw to protect her, to save her from death. He just killed nineteen people out of cold blood. While this Intersect was currently in control of her Chuck she was more afraid right now of what will happen when Chuck comes back. How will he react to the knowledge that he had killed so many people? She knew she would be there for him through everything, though she was still shocked herself. It was one of the things she was always worried about when Chuck became the 2.0 Intersect and started training to be an Agent. She didn't want him to kill people, to go against his being. She wanted him to remain innocent, or as innocent as one could be while associating with spies.

Sarah's phone rang then breaking her out of her thoughts and she stopped pacing. She blinked a few times looking around remembering then that she was in the Orange Orange. Grabbing her phone she saw Casey's annoyed face on the screen and she picked it up, not offering a greeting.

"Walker, get down here. Beckman will be on in five." He growled through the phone, hanging up before she could even respond. She lowered the phone from her ear and took a few deep calming breathes before turning to go to the freezer and down into Castle.

General Beckman was already on the screen by the time she entered the conference room. She spared a glance at Casey who sat at the head of the table and Chuck who stood at attention, eyes on the screen.

"Thank you for joining us Agent Walker." Beckman stated but without her typical flair. Sarah noticed that she looked tired and somewhat harried.

"I apologize General. Were you able to ascertain what is happening?" She asked. She watched as the General gazed at them seemingly sizing them up before talking.

"I have and it's not good as far as I can tell. The Joint Chiefs had authorized an upgrade on the Intersect from 2.0 to 3.0." She said. Sarah met Casey's eyes widened in shock.

"General, why weren't we told of this upgrade? That's significant information we need in order to operate." Casey protested finally standing up, ceasing further questions as the General raised her hand.

"I am well aware of this Col. and unfortunately I do not have an answer for you. I was not informed of this either." She stated.

Sarah looked at Chuck then, trying to gage what his reaction is to this news but he stood steady fast as before staring straight ahead at the screen. Her heart beat widely at the implications of what was being said.

"Well what does it all mean? What does this 3.0 do?" Casey asked and Sarah was grateful, unable to get any words out herself. The General visibly sighed warily and leaned back in her seat.

"From what I can ascertain it does everything that Agent Bartowski doesn't. That's almost the exact phrase that was used. It follows orders to the letter, it gets the job done, it kills, it reports to its superiors. It can work on its own." She said.

Nobody said a word, too horrified to say anything. It was a superiors dream. A soldier to do exactly as told without questions. The way the Intersect was made to begin with. But what did that mean for Chuck?

"And what about Bartowski? Is he a willing participant in this?" Casey inquired, his fists clenching. Again Sarah stared at the General trying to gage some answers from anything she's not telling them.

"From what I understand the Intersect 3.0 is a separate entity from Bartowski. Unlike the previous versions of the Intersect this one is not to work with the host but work in place of them."

"But what about Chuck? He's not going to have a choice in this? It's his body! It's his mind!" Sarah protested vehemently. She knew she was being insubordinate and was prepared for the backlash but to her surprise the Beckman didn't call her on it.

"The final part of the upgrade will fix the problem. There will no longer be any blackouts or time outs or whatever is happening right now." She told them. Sarah felt momentarily relieved at hearing it was almost over but Casey's low growl made her think twice.

"But who will be in charge? The Intersect or Chuck?" He asked surprising Sarah as she didn't even think about that. She stared at Beckman on the screen waiting as she read over some report in front of her.

"From this summary it states that the final upgrade will clear out the unnecessary programing and allow the Intersect to resume all operations." She said closing the folder. "The original date for the upgrade was scheduled to take place in two weeks but in light of recent events I've requested that it take place tomorrow."

"Is that wise General? The last update was, well, it was very hard on Chuck."

"I understand Agent Walker but I want this dealt with as soon as possible." Beckman stated surprisingly sympathetically.

"It is alright General Beckman; I am ready and prepared for the finale upgrade to my programing. Tomorrow will suffice." The Intersect stated, speaking for the first time. Everyone stopped talking and stared at him. Sarah wasn't sure what to say but she was with Casey as he growled in annoyance.

"You don't get a vote. You may be ready but that doesn't mean Bartowski is. You're are machine and he is not." Casey growled out angrily at Chuck.

To Sarah's surprise Chuck turned towards Casey lowering his arms from behind him and stared straight at him. She could see Casey's eyes narrow as he glared angrily at the thing that invaded his friend's body and mind.

"I assure you Col. Casey, Chuck will be fine. I will not allow any harm to come to my host." He stated with finality in his tone. Sarah watched for another moment before she moved to step in between the two breaking them up.

"Alright you two. If there is nothing else. I want you to remain in Castle until-"

"That will not be necessary General. With the update tomorrow I feel it would be more beneficial for Chuck to go home and prepare himself." Chuck stated, standing at attention once more. The General eyed him warily before responding.

"Except you are not Chuck Bartowski are you?" She stated matter of fact. Chuck stared at her for a moment before his eyes crossed slightly as if in a flash. Sarah stood near him alarmed at what was happening but too afraid to touch him quite yet.

The flash lasted for well over a minute with the three others holding their breaths and waiting for what was to happen. Finally after what felt like too long Chuck's face relaxed back to its regular features before his eyes blinked rapidly and he crumbled to the ground.

"Chuck!" Sarah called out as she fell on her knees next to him. She placed her hand over his neck searching for a pulse and sighed in relief at finding it strong and steady.

"What happened? Is the Intersect alright?" Beckman called from the screen. Sarah ignored her as she ran her hand through Chuck's hair, calling his name softly.

Finally his eyes fluttered a few times before finally opening and looking up at Sarah. He gave her a small wane smile as he reached up weakly and ran his fingers lightly over the side of her face.

"Hey you." He said softly. Sarah's breath hitched slightly as she stopped the sob that wanted to come out and just smiled down at him.

"Hey, how are you?" She asked him. He lowered his arm to rest on his chest as he looked around where he was, brows narrowing at seeing Casey's concerned face standing near him.

"Where…We're in Castle?" he asked confused slowly sitting up. Sarah reached behind him and with Casey's help got him up on his feet. She watched as Chuck looked around the room, eyes settling on Beckman as he took in his surroundings. "How did?"

"That's not important right now Chuck. What's important is are you ok?" Sarah asked him. She stood in front of him between Beckman and him and looked up into his eyes her heart fluttering happily at seeing his confusion and his love as he looked back down at her. This was definitely her Chuck.

"I'm, fine I guess. But, what happened with the mission? Did I get hit again?" He rolled his eyes then and crossed his arms. "I can't believe it. I got tranqed didn't I? Some spy I am."

Sarah wrapped her arms tightly around his waist and buried her face in his chest happily. She felt Chuck hesitate; probably confused by her display of affection especially in front of the General but he just wrapped his arms tightly around her back.

"Well, it looks like everything is alright for now. Agent Walker, Col. Casey, you are too keep a close eye on him and if anything seems amiss, deal with it and bring him back to Castle immediately. The update will take place tomorrow at 1030." With a final look at each of her subordinates General Beckman exited out without a final word.

Sarah stood there in Chuck's arms, not wanting to move, not wanting to show him how frightened of the situation she was, but she looked up from his Chest as she felt Casey place his hand on her shoulder. She looked into his eyes as he communicated to her in the way that they had grown to do over the years. She nodded her acquiescence and he turned to leave, giving Chuck a pat on the back as he did.

They stood there a few more minutes in the middle of the conference room, just holding on to each other. She didn't want to let go of him, afraid that if she did Chuck would disappear and the Intersect would be back in his place, but she knew they couldn't stay there. She wanted to get him home.

"Come on, let's go." She said placing a kiss on his chest before reaching around for her hand. She guided him wordlessly out of Castle and into her car. The ride was silent as she drove cautiously back to their apartment. She refused to let go of Chuck, grabbing hold of his hand the second they were in the car.

She knew that Chuck was aware that something was off. How could he not? He was so attuned to the world around him, and especially to her. She hated admitting it, though less now then before that he had always been able to read her, know how she's feeling, what she's thinking. She was thankful that he waited till they were home, safe in their apartment, thankfully alone before he breached the subject.

Chuck closed the door behind them as she walked over to the couch and he leaned against the door, the only light was the kitchen light that always seemed to be on no matter if someone was home or not. She sat down heavily on one end and stared back at him, hating that she knew she would have to tell him now when she didn't want to. She wanted to protect him, even if it meant from himself.

To his credit he didn't say a word. He had learned a long time ago that pressuring her into telling him something would not get the results he wanted. He had learned that being patient and being there for her would get her to tell him the information he wanted to know.

With this in mind she motioned for him to sit next to her on the couch and waited as he walked slowly toward her, seemingly somewhat stiff as he sat down on the couch. She immediately grabbed on this his hand and entwined their fingers together while using the other hand to tickle the top of his hand. She watched them as she thought about how she wanted to tell him what happened.

"Chuck, I have something to tell you. Ok, don't freak out." She started looking up from their hands to his eyes. He smiled brightly at her and let a soft laugh out.

"Sweetie, if you want people to not freak out don't start a conversation that way." He teased. But his smile faded as she looked at him seriously. She took a breath and held it in a few seconds before slowly letting it out, deciding on where to start.

"Remember this morning when you asked me, how you got home. You thought Casey brought you in?" She asked watching as he nodded his head. "Well the truth is he didn't Chuck. You actually did it yourself." She told him.

After that everything came flooding out, about his robotic actions the night before and the mission. She hesitated about telling him about the nineteen men he killed, not wanting him to feel the pain and remorse of doing something so horrible when he had no control over it. She told him of the upgrade that was done to him without their knowledge and worse of all, without his consent.

The look of horror on his face broke her heart as everything crashed down on him. He released her hand and stood up walking away several feet toward the television, arms crossed over his chest as everything sunk in. She waited patiently in silence for him, hating that she put him through this hurt but knowing he had the right to know.

They stayed like that for an indeterminate amount of time. As time went on however Sarah began getting more and more concerned. She didn't think she'd seen Chuck be so silent and still in her life and it scared her.

"Chuck, say something." She said softly staring at his back. He seemed to ignore her a few more minutes before he turned around slowly and looked at her. The tears in his eyes tugged at her as she opened her arms to him.

Chuck immediately went to her and embraced her. She held him close as he buried his face in her chest. She soothingly ran her hand in small circles over his back while the other hand gently toyed with the hair on the back of his neck. She fought hard to stop the tears from falling form her eyes, but she couldn't stop them all as a few escaped and fell slowly down her cheek.

Chuck sat up slowly after a while and placed his hands over his face. She could hear him softly sniffling as he tried to get his emotions under control.

"Why would they do this?" He asked through his hands. She shook her head unsure. Chuck lowered his hands then, giving Sarah a complete view of his red eyes and puffy face. "I've done everything they've asked. Why would they….I feel so violated." He shouted angrily covering his face again.

Sarah got on her knees on the couch and moved closer to him and wrapped her arms around his neck and shoulders, placing her head on top of his gently.

"I don't know Chuck. I don't know why they would." She whispered to him placing a kiss on top of his head.

Gently Chuck pushed her away and turned her body towards her and grabbed her hands. She looked at him curiously as he took staggering breaths to steady himself before looking deep into her eyes.

"Sarah, if…if this Intersect takes over, I want you to know that I don't-"

"No. No no no no." She chanted ripping her hands from his and standing abruptly up in front of the couch. "Chuck it will be ok." She assured him as he shook his head.

"Sarah I killed nineteen people." He said simply, as if that would explain everything.

"No you didn't Chuck. The Intersect did."

"Through me! It doesn't matter if it was a computer or whatever. It used me, my hands, my body to kill people. It was done against my will!" he argued. Sarah shook her head again and walked a few feet away before turning back to him.

"Tomorrow everything will be fine. It will be back to normal." She said decisively, seemingly trying to convince herself of it. However Chuck's bark of a laugh dissuaded the momentary reprieve.

"You don't know that. Neither do I. We know nothing about this upgrade Sarah. For all we know it's going to take me over."

"Don't say that Chuck. You don't know what will happen." She argued angrily coming towards him again.

"I don't but I've watched enough sci-fi to know the many options. And if that happens-"

"No."

"Then I don't want-"

"No! No Chuck no. just stop." She shouted covering her ears with her hands. She stood there shaking slightly with her eyes closed tightly. She wasn't sure how long she stood there but soon enough she felt Chucks larger hands on hers lowering them from her ears. She opened her eyes and saw the tears that fell freely from his eyes.

"I don't want to say it any more then you want to hear it but Sarah, I don't want to live like that. I don't want to be responsible for what horrors that the Intersect can release on people."

"Chuck…" she said desperately.

"Sarah I love you so much you have no idea. But I need you to be the strong one. I need you to stop it if I can't."

"No, I can't kill you Chuck. Don't ask me to do that." She pleaded.

"I don't want you to baby, I promise. I don't. But I don't want to be a prisoner. If it comes to that, if the Intersect is in control I want you to stop it. Promise me."

Sarah couldn't do this, she didn't want to and she couldn't. He was asking her to do the worse thing she could think of and she couldn't. But a small part of her in both her heart and her mind knew that he was right. That if the Intersect took over he would be a prisoner. His body would be used to do things that he would never do on his own and as much as she couldn't hurt him, she couldn't stand the thought of any more death being caused by Chuck's hands, especially when it wasn't Chuck.

"I promise Chuck." She said softly. Chuck grabbed both sides of her face and brought his lips to hers kissing her passionately, telling her through it how much he loved her and how much he knew it would hurt if she had to do it.

She pulled away hesitantly and looked up into his eyes.

"But not until I'm sure." She stated firmly.

"Sarah-"

"No. I understand but Chuck, I'm not going to take you out until I know for sure that I can't save you first. I'm not giving up on you Chuck Bartowski. I love you too much." She told him firmly. Chuck sighed sadly and shook his head.

"Sarah the things that-"

"I don't care. Chuck we will deal with it. But no. I'll end you if I can't save you. I promise you. But you have to give me a chance."

Chuck thought for a moment and she held her breath as she watched him before he nodded his assent. Her heart lightened slightly at that as she threw herself into his arms placing kisses all over his face. She knew he should rest, prepare himself for tomorrow but all she wanted to do was spend the night showing him how much she loved him, praying it will give him hope to hold on.

A/N: So...thats totally not where I originally saw this going but meh, there you go. Sometimes you write the story, other times the story writes you. I dont think this will be a super long fic though but you enjoy this chapter, and i'm off to attempt the next one. *takes deep breath* Wish me luck.


	5. Chapter 5

A/N: Thank you to my beta charahkids. And everyone should thank them too cause thanks to their brilliant brain storming this story is now gonna be a bit longer. I was totally going to do a quick death of it but charahkids broadened my creative thinking. Thank you to all those who have reviewed, I enjoy reading them and I appreciate your time it takes to read then review.

Chapter 5

Apprehension filled Casey as they walked down the hall of the CIA facility they had just left two days ago. He wasn't looking forward to this but as always he didn't have a choice. He was given an order and he would follow it, though if he were honest with himself, if Chuck decided he didn't want to go through with the final update than he would help get him out of it.

He didn't like this situation at all. Being a career military man and working with the NSA he was used to following orders and doing things with little to no information. The things he did in the name of his country would make the strongest of men or women shriek and cry in horror. However, there was something about this that nagged him deep down in his core.

He felt like they were being played with. That instead of using them for the greater good to stop terrorists and bad guys of all manner of things they were being used as a terrifying experiment with no regards to what the outcome could bring.

He'd be the first to admit that Chuck Bartowski was an annoying obnoxious man and that he would have no problem locking him away in a trunk for a few hours just to make him squirm. However Chuck had served his country honorably, being forced into it at first and had excelled at the challenges put before him better than anyone else Casey thought in his position would. But now he was being used as a lab rat.

When he first heard about the Intersect being uploaded into Chuck's brain he admits he didn't totally get it. He wasn't big on technology outside what was needed for him to get his job done efficiently and the idea of data being encrypted and then uploaded into someone's head like a computer hard drive baffled him. But like anyone who is forced into using the technology around them, he learned. And the more he learned the more fearful he got for Chuck.

He always knew deep down that the technology used for the Intersect could create something like this. Create some kind of monster that could overtake a human mind and take control of their bodies, willing it to do as it wishes without the consent of the person they were over taking.

While Chuck hadn't always been in control of the Intersect 2.0 he had no doubt in his mind that he would never intentionally hurt anybody. His emotions being all over the place so frequently the Intersect was more likely to not work at all then to go out of control.

However this 3.0 Intersect sounded terrifying. Not just for Chuck but for all involved. He didn't know exactly what it was going to do but he knew enough about the Intersect to know what it could do and that's what frightened him. And apparently it frightened Chuck as well.

Casey thought back to the conversation he had earlier that morning as he watched the technicians strap Chuck into the intersect chair and prepare him. Chuck had come to his apartment, obviously sneaking away while Walker wasn't looking at made Casey promise something that he'd rather not think of.

Casey understood Chuck's concern. The unknown of this Intersect and the actions it had taken in the past forty-eight hours scared the crap out of him. Casey was glad that Walker had told Chuck about the black out after the update and what had happened the previous day. They hadn't spoken about it, not really having the time to do so as neither wanted to leave Chuck alone for any amount of time, but he had wanted to tell Sarah that he felt she should tell Chuck the truth. The nerd deserved it. It was him that was doing these acts.

He could tell by the way Chuck looked at his watch that morning in his apartment that he was short on time so instead of mocking him or getting in a few jibes he just grunted and asked him what he wanted, and to his surprise, Chuck came right out and said it. No babbling, no crying, no lady feelings. Just straight out told him what he wanted.

"I'm not going to just shoot you Bartowski no matter how much pleasure it would give me." He growled out, sitting at his dining room table in front of his guns. He had gotten up early to clean them and care for them. One of his more enjoyable activities.

Chuck hadn't given up. He sat down heavily in the chair next to him and placed his hand over Casey's stopping him from what he was doing. Casey glared and growled a warning but Chuck kept his eyes steadfast and serious.

"I'm serious Casey. You saw what that thing made me do yesterday. That is not me. It will never be me." He told him. And Casey acquiescence. He's not a man that frightens easily but the events of the previous day scared the crap out of him.

"Why not tell Walker this?" He stated already knowing how well that would have turned out. Chuck took his hand away and set it gently in his lap and looked away for a moment.

"I did. I told her I didn't want to live trapped in my mind like that. That even if I wasn't really there I didn't want to be responsible for it. I couldn't live like that."

"You're assuming you'll still be there someplace Chuck. For all you know this machine will over right you and just take over." He told him. Chuck looked at him then at the look in his eyes caused his gut to twinge. It was sad and it was desperate, and Casey knew right then that Chuck was more than aware of that scenario.

They didn't speak for several moments each lost in their own thoughts. Casey went about cleaning his weapons and Chuck just stared off to the side out the window at nothing in particular. He wouldn't want to be in Chuck's shoes, not knowing what the future held. Not knowing if within the next few hours he would cease to exist.

"I'll do it." Casey said quietly, not looking up from his weapons. He could feel Chuck's eyes turn towards him but still refused to look up. "If Walker can't, I'll be sure to end it for you. I won't let you suffer as a monster."

And that was a promise he was going to keep no matter what. He understood Walker wanting to try to save Chuck first; he will be with her every step of the way helping her. But if or when the time comes and there was no hope of saving Chuck from whatever the Intersect 3.0 was, he would make do on his promise and he will stop him at all cost and end it.

Casey was brought back to the present by a loud shout from Walker. He watched as she pushed one of the techs away roughly who was in the process of restraining one of Bartowski wrists.

"You're going to hurt him." She said angrily. She undid the strap and then reapplied it, slightly looser than before but still tight enough to not allow Chuck much movement. Casey restrained himself from rolling his eyes and settled for his patent stoic glare.

When everything was set up the techs that were idling around them setting things up skedaddled, there was no better word for it, out of the room leaving Casey alone with Chuck and Sarah. He stood watch over them, eyes searching the room thoroughly as they conversed. He tried to shut them out but he couldn't stop over hearing Walker pleading with him to be ok.

He glanced over at them in time to witness their final kiss and embrace before she stood up and walked way. Casey could tell the way she blinked her eyes and how she was taking short breaths as she walked that she was trying to get her emotions under control. He wanted to break the tension she was feeling by making a comment but thought better of it.

He walked in front of Chuck, taking in his tired appearance as he sat in the chair. He was strapped on the wrists and ankles with a helmet like thing on his head and metal prongs holding his eyes wide open. It wasn't a pleasant sight, and he hoped against everything that this will come through alright, not wanting this to be his last image of Bartowski in his head.

He bent over to look him directly in the eyes. He watched as Chuck's soft brown ones stared back at his own blue ones. He wasn't sure exactly what he was looking for but whatever it was he didn't see it. He gave the kid one last nod, indicating he understood what he was to do before standing up at his full height and exiting the room.

Walking into the control room he looked out the window into the large white room beyond and waited for it to begin.

"Glasses." The tech in front of him that was controlling the Intersect computer called out to those around him. Casey took one last deep breath, and put his own protective glasses on, watching as everything turned slightly darker as he waited for the last update to take place, and hopefully, for his friend to come out of it alright.

He watched the screen next to the tech in front of him, the one with a camera in front of Chuck. The Tech counted down to three before everything went dark in the Intersect room for a moment and then it started.

The images seemed different from the previous updates. They were more abstract and less photographic. They had hues of blues and reds instead of being multicolored across the spectrum. They flashed and twirled as if trying to hypnotize the person watching them.

Casey watched the screen with Chuck on it, watching it for any distress he may display as he did last time. But none of it showed on his features. Chucks forced opened eyes were straight ahead and glazed over as whatever was encoded in the images were put into his brain. Something in the back of his mind tingled singling that something wasn't right but he couldn't place what it was.

The update seemed to last twice as long as any of the others, and at the end of it, the lights turned off bathing them all in blackness once more before turning on the lights bathing them in the whiteness of the florescent. Glancing at the screen one last time, seeing Chuck's glazed appearance still staring Casey quickly took off his protective glasses and followed Walker into the room.

"Chuck?" She cried out, crouched in front of him as techs removed the helmet and eye prongs but much to his distaste left the restraints on. He was about to bark they take them off as well when the door behind him opened and Director Johnson walked in with a small entourage.

"I wouldn't do that just yet Agent Walker." He stated with a smug smile. Casey turned and saw that Sarah had stood and was about to take off the restraints on his arms.

"What is the meaning of this?" Casey growled out trying to be respectful but still untrusting of this man. He stepped back slowly till he stood on the other side of Chuck in a protective stance.

Director Jordan didn't answer him as he stepped forward and looked down at Chuck. A slight shiver went down Casey's spine as he saw the look of absolute glee that was shown on his face.

"This is the dawning of a new time Col. Casey. Now we stop using cold war tactics and we begin to finally fight for the greater good of our country up front." He stated proudly. Director Johnson motioned to a tech behind them. Both Casey and Sarah turned around to see the back wall panels open and allow a large MRI machine be brought in.

"Mr. Bartowski, this is Director Johnson of the CIA. Can you hear me?" He asked and waited for a response. It took several moments but finally Chuck blinked a few times and began sitting up straighter in his seat. Sarah once again moved toward him to release him but was held back by one of the men who came in with the Director.

"Let him go! What are you doing?" She shouted as she fought off the man, but the Director paid her no mind.

"Chuck Bartowski, do you hear me?" He asked again leaning slightly forward to see Chuck's eyes.

"Chuck cannot hear you." Chuck's voice said looking straight ahead. Casey's heart sank slightly and he heard Sarah cry a soft 'oh god' at his words.

"And where is Chuck Bartowski?" The Director asked him. Chuck looked up at him then, expression blanked and eyes focused on nothing in particular.

"Chuck Bartowski is gone." He stated.

"No, no no. You're lying!" Sarah shouted at him before she turned to the Director. "What did you do? WHAT DID YOU DO TO CHUCK?"

The man that had grabbed her before reached out for her again but she took his hand before he could touch her and pressed down breaking it and pushed him back. The others who had come in with the Director stepped forward to restrain her but Casey stopped her by grabbing her arm and holding her back.

The Director stood next to Chuck facing them with his grimy smile still plastered on his face. He seemed pleased with the situation and it turned Casey's stomach.

"Agent Walker you will restrain yourself now or I will have you removed." He stated sternly. Director Jordan turned back to Chuck who watched him with hard eyes. "Will you attack if I release you?" He asked Chuck. The man in question paused for a moment as if thinking about it.

"It is against my directive." He stated mechanically. The Director rubbed his hands together gleefully before motioning for an Agent nearby to release him. Chuck paused for a moment as if getting his baring before standing up tall in front of the Director.

"Good good, very good. And tell me, who are you exactly." Director Jordan inquired joyfully.

"I am Intersect 3.0." He stated.

"And what is your directive?"

"To complete orders and follow through missions in order to protect the greater good of the United States." Chuck answered. Casey didn't like the mechanical way he spoke, knowing for sure now that whatever was happening did not bode well for anyone.

"And whose orders are you to obey Intersect?" The Director finally asked, causing Casey to growl at the excitement that seemed to roll off him during this entire experience.

"I am to follow the orders of Director Jordan of the CIA." Chuck answered, causing the smile on Jordan displayed get impossibly bigger. "And General Beckman of the NSA." With that the smile faded from the Jordan's face.

"You are to only follow my orders Intersect. Not that of the NSA. Do I make myself clear?" He bellowed. Chuck to his credit did not even blink at the shout.

"Operation Bartowski, also known as Team Intersect is a joint operation of the CIA and NSA respectively." Chuck recited. As grim as the situation was Casey couldn't help the small feeling of satisfaction at Director Jordan getting annoyed.

"Yes, well. We'll see about that." He grumbled, more to himself then for anyone around him. Casey made a note to contact Beckman and let her know of Director Jordan's intended exclusion of her on this as soon as he could. "In the meantime Intersect. These men have some test to run on you. Col. Casey, Agent Walker, if you would please." He motioned for the two of them to follow as he walked pasted them.

Sarah ignored him as she tried to approach Chuck only to be blocked by the other agents in the room.

"Let me near Chuck or I swear I will break every bone in your body." She threatened. The men to their credit didn't stand down from her threat, though likely they were frightened knowing her reputation she would have done it.

"Agent Walker, Chuck will be fine. They are going to do some tests. I wish to speak to you." The Director said from the door way. Casey sensing they would do no good here at the moment grabbed hold of her arm tightly and dragged her away towards the door with him.

He dragged her forcefully until they were clear of the room and the door was shut behind them. She then shrugged off his hand and turned around to follow the Director angrily.

They went down the hallway taking a few turns until they came upon a room with the name plate "Dr. Krinshaw." And entered.

The Director went around the desk and sat down; pulling out folders from the brief case he had been handed before exiting the Intersect room and put them in front of Casey and Sarah once they sat in the chairs in front of the desk.

"These are your knew orders." He stated to them. Casey glanced at Sarah curiously for a moment before reaching out and grabbing the folder as she did and opened it up. "It's basically the same as before but instead of staying in Burbank sitting idly, you two will be spending more time in the field."

"What about Chuck?" Sarah asked closing the folder, obviously not wanting to hear what he had to say.

"Agent Walker, please. With the Intersect 3.0 now in place we can now spend fewer resources and be more efficient at fighting the war on terror."

"Director, I don't-"

"You two will continue to be part of his team, but instead of being handlers or partners your jobs are mostly support and assessment."

"Director-"

"I know you two are used to getting your hands dirty but the Intersect is more efficient when given leeway to get the task done at-"

"What about Chuck Director Jordan? We have a life, a family. What did you do to him?" Sarah stated angrily as she slammed the folder down onto the table. Director Jordan stared her down for a few moments but backed off with a wary sigh as she continued. Casey knew he should say something at this point, not having said anything since this whole thing began, but he knew that sometimes being silent yielded the best results.

"I understand your situation Agent Walker." Director Jordan started.

"My situation? My situation is I'm in love with the man you seemed to have just turned into a machine." She spat.

"It had to be done. We need the Intersect. We need it at its fullest capacity and try as he might Chuck Bartowski just wasn't up to the task."

"So because he can't or won't do exactly what you want you think that's reason enough to take control of him?" Sarah asked incredulous.

"We did what was needed for the greater good of this country." Director Jordan defended.

"Do you have any idea or even care what you did? You violated his trust, his body. You violated his mind! Does this mean nothing to you? Does he mean nothing to you outside the Intersect?" Sarah defended passionately. Casey nodded his head in agreement at her words.

Director Jordan was disrupted from a reply from a knock on the door. He shouted for them to enter and a tiny technician came in with a folder and handed it to him. Sarah and Casey sat silently as the two conversed over whatever was in the folder. After a few moments the tech left the room leaving the three of them in a silence.

"Agent Walker, I understand what you are saying but the truth is, Chuck Bartowski is now gone." Director Jordan stated as he pulled out a few slips from the folder. He held them out for them to see. It was CAT scan images showing Chucks brain. There were large patches of colors all over it. Casey wasn't sure exactly what he was seeing, not being a doctor but he had a bad feeling about it.

"I don't….what does it mean?" Sarah asked him staring at the scans.

"These parts." He showed them various sections of the brain. "Are the Intersect. And this scan is when they inquired about Chuck Bartowski." This scan being shown was darker than the other. "From what the technicians can devise from these readings, Chuck Bartowski has successfully been erased."

Casey looked towards Sarah at that, eyes wide in horror. He watched her shake her head in denial and he wish that she could join her. He didn't believe it, didn't think it was possible. But then again he never thought any of this was possible until he was assigned here.

"You're wrong Director. And I will prove it." Sarah told him standing up. Casey stood up next to her ready to take his leave if she did. The Director gave a sad sigh that sounded false even to Casey's ears as he placed the sheets back into the folder and held it out to her.

"The proof is right there Agent Walker. We hesitated about informing you about this but the truth is you are one of the best Agents the CIA has and we need you on this. If you wish to continue to pressure a relationship with the Intersect we are willing to look the other way as long as it doesn't interfere with the work."

Casey quickly grabbed hold of Sarah's arm again as she tried to take a step forward. As much as he would like to smack the crap out of the Director as well but doing so would do no good at the moment. Right now they need to think and gather information before they do or say anything rash.

"Walker, let's go." He said tugging at her arm, but she refused to break contact with Jordan. Director Jordan stood up from the desk and buttoned his suit back up.

"I understand you're upset at the moment. The Intersect is to stay here for the time being while we run some tests. After that we will ask for your decision. If you agree then we will send him home with you for the cover and will work and separating him from those around him."

"Like hell." Sarah spat. Casey responded to her outburst by squeezing her arm harder.

"We will consider your offer Director. Thank you for your time." Casey muttered dragging Sarah with him.

Once again after they exited the room Sarah broke out of his grasp and glared at him before stalking off. He could tell by the way she looked back and forth and in every open door they passed that she was looking for some sign of Chuck. He doubted he would be anywhere they would see him at the moment as they knew Sarah Walker would want to take him.

She marched angrily in front of him and out the door to his car. He gave a silent sigh of annoyance and unlocked the door for her grimacing as she got in and slammed the door. He wasn't sure where to start but he waited until they were several miles away from the facility to start talking.

"We need to come up with a plan." He said simply. Sarah seemed to ignore him for a few minutes and stare out the window at the passing scenery.

"I'm not leaving him Casey. And I'm not going to kill him." She told him firmly, leaving no room for argument. "I know he told you to, but I won't let you kill him either. Not till I know I can't save him."

Casey watched the road not responding. She was right to believe he was thinking about his promise to Chuck. He understood it and he will end him if he has too. But he was not a man of science or medicine and he wasn't going to just give up because a CIA Director showed him pictures with colors as proof of his friend being gone.

"I know your lady feelings are out of control right now Walker but I need you to put off thinking like a girlfriend and think like an Agent right now." He told her honestly. He ignored her glare she shot at him at his comment.

"My boyfriend was just turned into a mindless robot killing machine against his will and the CIA offered me to keep sleeping with him as long as the job gets done. I just lost the person I love the most." She spat at him.

"You haven't lost him entirely yet. We still have a chance." He argued back, ignoring her other comments. She gave a laugh of derision as she stared back out the window.

"And how is that Casey?" she asked sadly. Casey pulled up to his parking spot at his apartment in Echo Park.

"We do what we have to. Starting with using whatever resources we have available." He pointed out turning off the engine.

"In case you haven't noticed Casey our resources are the ones that did this too him. Any inquiry will not be met easily." She said unbuckling her seat belt. Casey looked around him, spotting Ellie and Devon's car.

"Then we use resources the CIA or NSA doesn't have in their pockets. Ones that would do what they can to help Chuck." He turned toward her giving her his best lopsided grin. "It's time we tell the Woodcombs the complete truth."

A/N: So this weeks gonna suck a bit starting with my work's holiday party. But it gave me an idea depending on how awesome or unawesome it actually is. They have a "murder mystery" theme going this year. I may write a short story xmas Buy More style like that. I'll let you know how the party goes and how drunk i get.

Peace Yo!


	6. Chapter 6

A/N: Thank You to my fabu beta charahkids. He's awesome.

Disclaimer: I'm not a doctor or a scientist everything in here is BS and made up exclusivly for my story. Pretend its real.

Chapter 6

Everything was going too fast for Sarah as she began walking through the gate toward Devon and Ellies apartment. Just the previous night she was wrapped up in Chucks arms, safe and secure if not a little frightened at the prospect of the next day and now here she walked towards his sisters place to spill all his secrets to try to get help for him.

She felt like she'd been doing this for days and weeks not the mere hours it's been. In the past few hours she had, according to the Director of the CIA lost her boyfriend to some computer that was in his head and was being offered a roll as a supervisory analyst on a team that would have him doing missions on his own.

She imagined what any other girlfriend would feel or do if they were in her shoes. They would probably be devastated and crushed. Would feel their hearts being ripped out and want to die. They would probably scream and yell, holler at the sky and swear at god for the unfairness of it all. She wanted to do that, she felt that.

But Casey was right; she had to think like an Agent right now and not a girlfriend. She was trained by the best at the CIA farm to push emotions aside and get the job done and she knew she had to do that right now if she had any hope of saving Chuck. She wasn't like every other girl out there. She was a spy and she had to act like one if she wanted Chuck back. She told herself she would not allow herself to fall apart over this until the end was certain and it was over. Till then, she'll be Chuck's kick ass ninja girl.

She wondered if Casey noticed the change in her, the steeling of her mind as she felt herself stand up straighter and her face relax into the cool confident Agent Walker personal. She felt his eyes on her as they walked around the fountain and stopped in front of the Woodcomb's door. She gently swiped under her eyes to remove all traces of tears and braced herself for the confrontation.

"Good work Walker." Casey said quietly next to her. She glanced at him once before raising her hand to knock on the door. They waited several moments before they heard movement on the other side and finally the door opened reveling Ellie. Her face lit up surprised as she greeted them.

"This isn't a social call Ellie." Sarah said briskly as she pushed her way inside. She saw Devon start to stand up from his position he was lounging on the couch and she raised her hand and indicated his hand and indicated that he should stay sitting. "You might want to sit down Ellie. We have a lot to tell you."

Ellie closed the door behind them and looked alarmed. Sarah wished she could alleviate whatever fears were running through her mind but she couldn't. Whatever Ellie was thinking was going, on itcouldn't compare to what was really happening.

Sarah took the big chair at the end of the couch while Ellie and Devon sat next to each other near her on their end of it. Casey had walked to the front of the living room and stood stoically in front watching over what was going on. Sarah sighed inside realizing that he was most likely going to make her take lead on this.

"Just tell us what's going on Sarah. Where is Chuck?" Ellie asked worried. Sharing one last glance at Casey, Sarah began unspooling all Chuck's secrets to his sister and brother in law. She felt bad at doing it, hating herself for needing to, but she hoped that when he came back to her he would understand her need to do so and forgive her.

"Ellie, before I tell you that I need to confess, Chuck didn't quit spying." She said and paused waiting for the inevitable explosion. When none came she was at a loss and slightly confused so she continued. "He wanted to Ellie, I promise. He tried to quit."

"If he wanted to quit then why didn't he? Why did he lie instead?" Ellie asked, anger brimming underneath her question. Sarah met Casey's gaze, silently communicating before turning back to Ellie.

"What I'm going to tell you is top secret at the highest level. Just telling you know is considered treason and I could go to prison for the rest of my life." She said seriously watching as Devon held on tighter to Ellies hand.

"And this thing has to do with my brother?" She questioned incredulous. Sarah nodded her head and sat further on the edge of her seat, hoping her body language will help convince the two that this is not a joke. "Alright, I'm listening."

Sarah nodded again and took a deep breath and focused her mind. Every fiber of her being resisted against telling them, her training telling her to stop, to keep her mouth closed and just leave. Divulging this information will get her in more trouble then she could imagine but she had to do it. She had to for Chuck. And even if nothing came of this, and Chuck truly was lost it wouldn't matter anyways. She was lost without him now and any life without him would really not be worth living anyways. Whether it is out in the open and free or in a jail cell.

"I know it's going to sound crazy, and I know you'll have a ton of questions but time is of the essence here so please, just, let me get this out." She started. She was surprised when Ellie moved closer to her and took her hand, squeezing it comfortingly.

"Just tell me Sarah. I need to know what been going on with Chuck. He's my brother, and I love him and I've been so worried about him for a long time." She said causing Sarah's gut to flutter with guilt.

"It's…Well, your father created this computer that can embed encoded images inside someone's mind. It was originally scraped as nobody could handle it but four years ago Bryce Larkin broke into where it was stored and sent all of it to Chuck who saw it and now he has all the government secrets inside his head that he can flash on." The words tumbled out of her mouth scattered as she told Ellie the tale. She wanted to tell her more eloquently but she was fighting her own mind and will just to get the words out.

Ellie and Devon looked at each other for a moment, each trying to gage how much of that the other got before turning back to Sarah with their mouths agape.

"What?" Ellie finally asked. Sarah swallowed hard and began again.

"It's called the Intersect. It mines for patterns and such so we can better stop the bad guys from doing well, bad things. It's all technical and a lot goes with it but the point right now is it's in Chucks head. He couldn't quit spying because the government would not let him. He's the most valuable resource we have in the intelligence community." She watched Ellie as she processed what she just told them with bated breath, hoping that they at least got part of what she had said.

"Ok, so what does that have to do with Chuck now? Where is he?" Ellie finally asked after several minutes of silence. Sarah couldn't help the relieved smile cross her face over having Ellie understand, or at least seem to understand the importance of what was going on now. They didn't have time to go over every single detail of what's been going on for the past four years, they had to help Chuck.

"Chuck is currently being held in a CIA facility ten miles out. He had been receiving updates to the Intersect the past few weeks; only they weren't updates like we were told. It was an upgrade from 2.0 to 3.0. We weren't told about the upgrade and for good reason." Sarah explained.

"And why not? This doesn't sound like something that should be taken lightly. The human mind isn't a toy to be messed with and it sounds like that's what the government has been doing to my brothers." Ellie stated, her voice raising slightly in anger. Sarah couldn't blame her, she too was pissed off that her government, the one she swore her life to protect and work for would do something like this.

"The Intersect 3.0 would take over Bartowski and wipe him out so only the Intersect would survive." Casey piped in at last. At Ellie and Devon's loud exclaims of disbelief Sarah couldn't help but glare over at her partner for his lack of tact. For his part he just shrugged and continued to stand stoically.

"What is he talking about Sarah? Chuck can't be gone." Ellie proclaimed. Sarah squeezed her hand that was still in hers and scooted closer to her.

"I don't know if he's gone Ellie. We were showed these CAT scans as proof that he is but we don't know if they're true. We don't exactly know how to read them." Sarah admitted, holding out the folder.

Ellie stared at her open mouthed for a moment before she grabbed the folder and opened it up, flipping through the papers and scans inside with Devon looking over her shoulder. They spoke in quiet voices using medical terms that were vaguely familiar to Sarah that she picked up over the years of espionage and television with Chuck but had no clue what it actually meant.

"What are they doing this for? I mean what's the point of this 3.0 taking over?" Ellie asked finally, still looking at the scans.

"They, the CIA specifically that we know of, doesn't feel Chuck is as effective as he could be." Sarah explained.

Ellies eyes narrowed confused. Sarah knew that Ellie was thinking about how impossible that would be. Chuck to the eyes of the world may not have been living up to his full potential, or any of his potential at all but Chuck still did everything that was required of him with the best of his abilities.

"How is that possible?" She finally asked. Again Sarah looks towards Casey, wondering how much or what exactly they should reveal.

"Your brother is a lot of things Ellie but he is no killer for one and that is just one of the issues. They want an Intersect Agent who doesn't have the moral compass your brother has and will get in there and do whatever it takes to get the job done. Bartowski is a damn fine Agent in his own right. His outside the box thinking has saved our asses and the asses of everyone in this country and even the world on many occasions." Casey jumped in.

Sarah felt her heart lighten at Casey's words. He was such a gruff guy that any kind of praise, even to her had a tendency to fill her up. But hearing him talk about Chuck in such light was a change and delight. She always knew he secretly liked Chuck but just wasn't able to express it outwardly.

"Then what's the problem? It sounds like he was doing his job?" Devon cut in eye brow quirked up.

"The problem is Captain that he does it in ways that's against protocols. He achieves the same end results but at the expense of the rules. Missions should be faster, cleaner, leaving less open for problems to arise. And your brother, as good as he is does not do it." Casey explained.

"In our world Ellie it's more efficient to just kill the people in our way to achieve the end results. And unfortunately collateral damage is needed in order to achieve that, and that's not something Chuck accepts. It's one of the reasons I fell in love with him." Sarah admitted, looking away from them for a moment.

"So what you're telling me is that the government has decided to take over my brother's body by uploading a computer program so that he'll be a more effective killing machine for them?" Ellie surmised closing the folder roughly. Another glance at Casey and seeing him nod was enough of a confirmation that she effectively got the main part of it.

"That's harsh dude. Chuckster is the nicest guy ever. If they wanted something more effective maybe they should have put this 3.0 into another agent or something." Devon suggested sitting back against the couch.

"Well…you see…It's…" Sarah started. She was beginning to feel they were getting slightly off topic and delving too deep into the intersect, there was still a lot of stuff that even she didn't know being as it was classified way beyond her pay grade. "Not important. The point is, Chuck has it."

Ellie glared at her for a second before leveling here glance back to the reopened folder. Sarah felt her spine shutter at the angry glower Chuck's sister gave her. They had talked and for the most part Ellie had gotten over the whole thing with them lying to her for almost three years but still, whenever anything spy related came up Ellie would still give her the angry stink eye that would make Sarah, the kick ass ninja of Chuck Bartowski want to cower in a corner and hide.

"It is important. It all is. It makes no sense to not just use someone else if that's what they wanted instead of taking someone and transforming them." Ellie bit out.

"It's Classified Woodcomb." Casey barked out causing her glower to turn to him instead.

"If I'm not mistaken all of this is classified John. And If I'm going to help my brother I need all the facts I can get. And that includes why him when there are other more qualified people out there." Ellie told them pointedly.

Sarah thought for a moment before she answered. Ellie was right. Her agent self was kicking her all to hell for just telling them what she has so far. She'd been working with Chuck since they got together to realize and work out that there really is not two sides of her. There is just Sarah Walker, but right now she felt the difference and she was fighting hard to break down that wall. She wished with all her heart that Chuck was there to help her.

She looked up from her chair to Casey who still stood steadfast in his soldier stance in front of them, with arms crossed and a stoic look upon his face. She pleaded with her eyes to tell them, hoping that with Casey's backup on this her Agent self would back down a bit. He glowered at her for a few more moments before tipping his head in acquiescence. She gave a silent sigh of relief and felt her Agent self retreat a bit.

"The Intersect can't be handled by just anyone. They had earlier testing's about five years ago that resulted in people going crazy or dying." She paused letting it sink in for a moment. "I don't know what Chuck told you about Stanford but the teacher who had him expelled taught a class in subliminal messaging. It was to test people's retention rate and he reported it to the CIA."

She paused there swallowing hard at the next part. The part she hated. The part that included Bryce. The part where she completely stopped trusting him and questioned everything he ever did during their time together and after.

"All he said was he was doing great in the class. And that's what caused the investigation that got him expelled." Ellie told her. Sarah swallowed again hating to tell the next part.

"He did do excellent and that was the problem. By then Bryce, his roommate was already recruited into the CIA. He had somehow found out about a secret project that Professor Fleming was involved with. It's a military operation called 'Project Omaha'. Because of Chuck's excellent scores he was a prime candidate for this and according to Fleming they weren't going to give him a choice. They were going to force him into the project." Sarah stopped then and reached out to the glass of water that was sitting there on the table. She didn't remember where it came from or if it was for her but she was grateful for the cool liquid going down her throat.

She watched Ellie as she put the pieces together in her mind. Watching her expression go from perplexed to realization to anger. She knew those feelings well. She had gone through the same as she watched the disc of Bryce trying to convince their teacher to leave Chuck out of it.

"So no matter what they were going to get my brother involved in this Intersect thing, whether he willingly participated or not." Ellie said, not making it a question.

"Yes. But Bryce stole tests and blamed Chuck for them. It got him kicked out of school but it invalidated his test scores and got him out of the line of the CIA. He saved Chuck, though now…"

"Now he's the Intersect so it only drew out time. " Ellie finished for her, picking up on it. Sarah nodded her head and sat back into the chair feeling tired. She was done talking, she didn't want to do anymore. Now she wanted action. Sitting around telling stories was well and good but she wanted to be out there with Chuck helping him.

The silence stretched on for several minutes, each person lost in their own thoughts. Ellie stared at the scans deep in thought as Sarah watched her. She wondered what the elder Bartowski was thinking and wishes she would tell them.

Ellie was so much like her brother sometimes. They have no problems expressing themselves but they both know how to hide what they were thinking from others very well. Sarah suspected that they got away with it so easily because of how much they share and express. When one is so open, nobody really bothers to do dig any deeper, something that she's been guilty of herself in the past. She's learned that's how Chuck hides his pain from others, and she hated it. But she couldn't fault him on it considering how closed up she was naturally and all the time.

"Well…" Ellie began as she scooted away from Devon slightly to sit up on the edge of the couch to use the coffee table. "I don't think he's gone." She announced, causing a bolt of hope to shot through Sarah. She immediately sat up further and got on her knees on the floor next to Ellie.

"How, I mean, they said he was." She said looking down on the scans and trying to see what Ellie did.

"Well, I don't have any proof Sarah, I mean, this technology is way over my head but look here." She pulled out the top scan that had red and yellow all over. "It's said that theoretically we only use 10% of our brains. It's not really true, we use more but it's just not detectable or we don't use the portions of our brains all the time. Now this area here, the largest spots shows increased activity at the time of the scan.

This is what I believe the Intersect is. It's a computer so it would use a large portion and the area it's at makes sense. But look over here." Ellie pointed to the other side opposite the red blob and pulled out the other scan. "This portion of the brain isn't really use much for stuff. We don't even know what it's for right now but look at the red and yellow spots here, and then on the other scan."

Sarah looked at both scans for several minutes trying to follow but she just kept getting lost. She looked up at Casey who gave her a shrug indicating that he had no idea what Ellie had just said either. She sighed loudly in frustration and covered her face in her hands resisting the urge to scream really loud, or at least to cry. She was over her head and she knew it and she did not like the feeling at all.

"It's ok Sarah you don't need to know all this it's just…" Ellie stopped and waited for Sarah to lower her hands and look at her again. "Trust me, I know my neurology and I think somehow, Chuck was push into another part of his mind. Someplace out of the way of the Intersect but still there." She said.

"How can you be sure Ellie?" Sarah asked her softly. Ellie reached down and placed her hand on Sarah's back and rubbed small circles soothingly.

"Honestly Sarah I'm not. I don't know any of this technology. It's just a theory, but it's the only one we really have right now until it's disproven." She told them. Sarah stood up then, wrapping her arms around herself tightly as she walked a few feet away to look out the window into the courtyard, across to her own home. The one she shared with Chuck.

"How can we prove or disprove this theory." She said simply to no one in particular.

"That's part of the problem Sarah. There's no real way to prove it. I can do some testing on him but that would require his participation and cooperation. But it doesn't mean that it will be conclusive." Ellie pointed out as Sarah turned back to the room. Casey gave a snort at that and the look on his face expressed exactly what Sarah was thinking, that it wasn't going to happen.

"I don't suppose we could just ask him." Devon said looking between Sarah and Casey. "I mean, if anyone or anything would know if Chuck really is gone it would be well, that thing in its head wouldn't it?"

"And what exactly would give you the impression that it would tell the truth or cooperate with you on that? Its loyalty is to the CIA it's a program." Casey growled out sinking that idea in the hole with a death stick. But Sarah was watching Ellies expression instead of listening to Devon or Casey.

Ellie's expression went from doctor mode to hopeless to curious in the span of a few minutes. Sarah could tell that something had crawled into her head, an idea that could prove useful but had yet to share with them. Again, Sarah hated when the Bartowski's did that.

"What is it Ellie?" Sarah asked not able to wait any longer for Ellie's epiphany to come out on its own. Ellie took a few more moments to gather her final thoughts.

"This might sound crazy, and I'm way embarrassed to say it, but, I've spent three decades with my brother and Morgan watching sci-fi stuff. This Intersect, isn't just a computer, it's an artificial intelligent being."

"Babe, really? Like a thinking robot?" Devon said incredulous but Ellie shook his comment off.

"It would have to be to live in a human environment. A computer program while it can learn is still restricted by its programing. It's still limited by the space it has. But in a human body, a human mind it would have to be able to adapt, to grow and learn. Otherwise it would be ineffective. Like leaving Photoshop open on your computer and expecting to make graphics for you on its own."

"Ok, I gotcha El, but I'm not following what you're getting at." Devon said thoughtfully.

"If it's an AI then part of Chuck has to exist in it as well. Look at this report." She pulled out a stapled form. "They've been putting this in his mind for weeks. It says that the final upgrade portion was completed the day before yesterday and that todays was more of a maintenance update." She read.

Sarah grabbed the report from her and read them, feeling stupid that she hadn't thought to read them before. She internally kicked herself for yet again letting the girlfriend side of her take over and ignores the Agent side. Agent Walker would have never missed this. Agent Walker would have read every damn thing in the folder before going to another source.

"So you're saying this program has been operating in Bartowski for several weeks?" Casey asked, starting to sound just as incredulous as Devon. But Sarah held the paper up to him.

"It makes sense Casey. It was completed the other day when it first took over, and then last night on the mission. Maybe it's been learning from Chuck." Her voice was starting to raise as the pieces began coming together.

"And what makes you think that Walker? He killed nineteen people." Casey growled out taking a step closer to her. Sarah thought for a moment her eyes glazing over for a second as she replayed the horrible night in her mind.

"He called me Sarah." She said softly. Casey quirked his eye brow confused and grunted a soft noise. Her eyes focused back on him. "He called me Sarah, Casey. He said "they were going to kill Sarah." He looked directly at me and said "are you alright Sarah.""

"Walker, I don't-"

"If it was just a program it would have called me Agent Walker, or Sarah Walker or something more official. It called me Sarah, like it was familiar with me." She stood right in front of him desperately trying to get him to see along her line of thinking. She could tell the moment he caught on by the way his eyes widened and moved back and forth quickly.

"He kept saying "Chuck is fine." He said, Sarah nodded quickly excitement and hope filling her. They were broken from their conversation by the sound of Devon clearing his throat.

"This is nice guys but what does it have to do with…you know." He asked still confused. Sarah made eye contact with Ellie and she could tell by the look on her face that she caught on as well.

"What they're saying is confirming that the program has been learning from Chuck. It's learned from him." Ellie said staring at Sarah.

"And it would know what the CIA has planned for Chuck. It could be possible that the program still has him." Sarah finished for her, sitting down heavily on the chair she had vacated not too long ago. "Now we just need to get ahold of it and talk to it." She said, feeling tired now.

She watched as Casey walked around the chair and towards the door, stopping before opening it.

"Yeah, we're screwed." He said, before exiting.

A/N: Ok. So, I really hope you guys don't mind but I'm probably not going to post another chapter till after xmas. I'm still going to write but i want to take the time to really get into the story and know wtf i'm doing. That and come on...its the holidays. I plan on sitting on my ass during my 4 day weekend and playing video games and watching Chuck.

Though I'm still considering a holiday short story of Chuck verse...would that be too cliche?


	7. Chapter 7

A/N: The not anticipated Chapter 7. I had it beta'd and ready to go on sunday but i forgot about it. Sorry. Thank you to charahkids for fixing it up!

Chapter 7

Director Jordan circled around the Intersect who was currently standing in the middle of his borrowed office at attention. His eyes were staring straight ahead, showing no indication of what was going on around him. But the Director knew differently. He knew that behind those glassy eyes data was being processed and crunched at a speed rate way beyond any human's comprehension.

The Director had a gleeful smile plastered on his face. Like a kid at Christmas who got exactly what he wanted and couldn't wait to play with his new toy. He was ecstatic that the project had gone off so well with only a small hiccup during the last stage. It didn't matter anywise, by then it was too late and the Intersect had already been successfully completely uploaded into Agent Bartowski.

There was nothing that could have been done at that point. The program had been successfully ingrained for weeks, studying its surroundings and learning. Learning about everything and processing it for later use.

Director Jordan originally wanted to have everything uploaded and ready to go the first update out. However the Dr. Krinshaw had argued against it. As much as he hated to admit it the little doctor was right. It was too much information at once for any human mind to absorb on top of that the doctor was adamant about letting the program have time to feel its way around. To learn about how humans operate so as to blend better amongst them making missions more successful, covers more realistic.

He just hoped that the thing didn't pick up on any of Agent Bartowski's more annoying nuances.

He completed his inspection by standing directly in front of the Intersect, looking directly into his glazed eyes. He stared into the soft brown orbs contemplating on what his next move should be. He knew that once word got out to the NSA, to General Beckman he will be forced by the higher ups of the agencies to play nice and share their new toy.

He had no doubt that General Beckman already was aware of what was happening at the moment with Agent Walker and Col. Casey being such loyal agents of hers. He was secretly surprised that he hadn't gotten another angry visit or at least an angry call from the General regarding the status of her third Agent. It was only a matter of time though he knew.

"Sir, Agent Walker and Col. Casey have arrived and are on the way up." His assistant announced hanging up their phone. Director Jordan didn't acknowledge him as he continued to stare up at the Intersect.

"Guess it's time to assemble the team hmm? Ready for a test Intersect?" He asked it. He watched as the eyes glazed further in processing before it answered in an affirmative. It took a lot of his willpower not to cheer and clap his hands eagerly like a seal at the Intersects effectiveness so far.

His attention was finally drawn away when the door opened and both Sarah and Casey walked into the room, faces impassive as they looked around at those assembled. He watched eagerly at the way Sarah took a cautious glance over in his Intersects direction, quickly taking in his stance and appearance.

Though she was under his command he was very wary of Agent Sarah Walker. He was well aware of her status as his predecessor's wild card enforcer. He had met her several times before, always in the presence of Langston Graham. He knew that Langston had information about him on some of his sketchier dealings and he was always cautious around Agent Walker, not knowing exactly what Graham may have told her.

He made a mental note as he watched her to put the Intersect on high alert and possibly have it eliminate her if needed. She was a compromised agent, falling in love with his new toy. He wasn't stupid; you didn't get to where he was today being so. Sarah Walker was a highly trained Agent, one of the best in the world. And her being compromised with the host of the Intersect did not bode well for him.

It was a cardinal rule of spies to not fall in love. Not only because the next second they are together they would either have to leave them without notice or kill them, but Agencies frowned upon it because it puts doubt on their loyalty. An Agent in love is more likely to turn against them to save their love. They are unpredictable, and very dangerous. And Agent Sarah Walker was the most dangerous of them all.

"Agent Walker, Col Casey thank you for joining me." He stated finally stepping away from the Intersect to walk around the desk. "Please have a seat." He said as he himself sat down in the big chair. He watched them silently for several moments, taking in their professional appearances and demeanors.

"We've considered the orders and have decided that we would like to be a part of it." Sarah stated stoically. He felt her steely blue eyes on him and he wanted to shudder at how deadly they looked.

"Of course it wasn't exactly and option to decline, but I'm glad to see you came about." He stated back at them, watching their stiff postures as they sat across from him. They were locked in some kind of game of mental chess. Everything said and done had to be strategic in order not to tip the other into their thoughts or plans.

"Of course Director." She replied back. She sat straighter in her chair and crossed her left leg over her right, exuding confidence and composure. He was sure a lesser man would cave under her icy stare, but he didn't. He was prepared for it.

"Well, I'm glad you decided in any case because we have a mission for the three of you." He stated watching their expressions for any disagreement. But both agents watched him impassively. "It's a simple mission but we wish to test out the Intersect-"

"Chuck." Sarah said, interrupting him. He looked up from the folder he was looking at making eye contact with her.

"What was that Agent Walker?" He inquired, knowing full well what she had just said. She didn't cower under his own hardened stare, if anything with a quirked eyebrow he almost felt challenged.

"His name is Chuck." She said plainly. Director Jordan gave a false saddened sigh and lowered his folder, steepling his fingers together.

"I understand this is hard for you Agent Walker, but, I'm sorry. Chuck Bartowski is no more." He stated, attempting to sound sympathetic but failing even to his own ears.

"Well you don't want to go around calling him The Intersect do you?" Casey jumped in finally, looking over at the thing in question. "If that's the case you might as well put a big bow with a card to anyone who wants it."

Director Jordan took a deep calming breath, hoping it looked more like he was considering their words and not that they were trying his patience. He didn't really want them on the team but as they were already on it, he was well aware that Beckman would at least fight tooth and nail to keep them all together. Being the most successful team in possibly the whole history of international intelligence did give them some advantages and leeways.

He looked over at the Intersect, which still stood at attention and stared off at the wall behind him. He liked this version of Bartowski better. He hadn't met him before but just from reading the reports he seemed like an exhausting, talkative and overly emotional guy.

"Intersect, what say you?" He asked it. The Intersect finally turned its head to survey those around him before answering.

"It may be prudent to continue to associate the cover name Charles Carmichael when referring to me as to not give away imperative information." He stated. Director Jordan barked out a laugh and slapped his hands together excitedly.

"That's a good point Intersect, or Charles I should say. Very well, you shall now be referred to as Charles Carmichael." He said gleefully before turning back to the two agents in front of him. "Now on to the Mission."

Sarah and Casey reached out across the desk to grab the two folders that Director Jordan was holding out for them. They opened the folders to see the mission parameters and making note of their roles.

"We're to be observing? Not participating?" Casey growled out in disbelief looking over at Sarah who was still reading the file.

"Yes. We want to see how well the Intersect, I'm sorry, Charles here performs. You two will be his eyes and ears in the surveillance van while Charles goes into the compound and retrieves the flash drive back."

"You're making it sound easy Sir, but according to this the place is swarming with enemy agents. How is Chuck here going to get in and get out alive with no back up?" Casey closed the file in his hands and looked at the Director disbelieving.

Director Jordan sat back in the chair, placing his hand under his chin he watched the two agents in front of him curiously. He agreed it was difficult and he was slightly concerned about it. It wouldn't look too good on him if he lost the Intersect after one mission. However, he genuinely believed that the Intersect could handle it without any assistance.

"The Intersect is a highly intelligent machine. I'm sure it will perform beautifully. And if push comes to shove, you two will be there as backup if needed. You're to go after it tonight. Take Charles to your base and put it together. Report to me immediately upon completion." He ordered.

With that Director Jordan stood up and held out one last folder out to which Chuck reached out to grab it. Not bothering to read it he placed it at his side, continuing to stand at attention.

"Good Luck."

The ride to Castle was silent. It wasn't a matter of not knowing what to say, it was they wanted to say too much. There were so many questions and unknowns to both Sarah and Casey but they weren't sure exactly how the Intersect would take them. It was a tool of the US government and as such it could and most likely would report them to Director Jordan if it felt it needed to, so they sat in silence and drove along the highway in silence.

Sarah herself wanted nothing more than to go to Chuck, to wrap her arms around him, kiss him and hold him tightly while she pleaded with the machine that took hold of her love to release him. To tell it that she loved the man who the body belonged to and how wrong it was that it took him over. She doubted the machine would care, not being human and having human emotions but it's what she wanted to desperately to do.

However she had made the decision to stay strong and play the Agent for now. To lower the defenses of the Intersect and those around him. They wanted to gain its trust, make it think that they were loyal to it and to those it reported to. It was a decision she didn't want to make but after listening to both Casey and Ellie, she had decided to follow.

She had been very surprised after Casey suggested it that Ellie whole heartily agreed. For a moment in time Sarah felt alone and her mind immediately began making plans on her own to take care of this. However Ellie had surprised her, knowing exactly what Sarah was wanting to do and admitting that she too felt that they need to fight hard for Chuck. However they needed to be cautious now. Nobody knew what was happening or how this computer worked. They needed to gather more intelligence on it before they can form some kind of plan.

They were right; she couldn't be the lovesick girlfriend who lost her boyfriend right now. But she couldn't be the other person either. She couldn't be the Agent girlfriend. She couldn't go in and kill everyone who did this to her Chuck to try to get him back. She had to play the calm Agent. She had to play Agent Sarah Walker, loyal spy of the CIA and NSA.

Suddenly she felt split into three people and she wondered which one in the end would win.

Pulling up to the Orange Orange, Casey pulled up to the back loading dock as to avoid anyone from the plaza seeing Chuck. If it were anyone else it wouldn't have been a problem but Chuck was well known around there and everybody liked him and found him easily approachable, something that would not be a great idea at the moment.

Sarah stepped out of Casey's car first, closing the door as she watched as Chuck got out from the back and looked around their location. She thought she saw a glimmer of recognition in his eyes but dismissed it. Of course he would recognize it. He doesn't have amnesia, just a computer program in his brain.

He followed them silently as they led him into the back way into Castle and into the conference room. He walked around the equipment in the room before his eyes finally settled on the screen ahead where Beckman normally appeared standing at attention once again.

"Do you need anything Chuck?" Sarah asked him standing off to the side. He turned his head and looked at her, or through her she felt, before turning back to the black screen.

"I do not require anything at the present time." He stated. Sarah nodded her acknowledgement and walked away, leaving him there to find Casey.

She found him in the armory pulling out weapon and preparing them for the mission tonight. She watched him as he meticulously checked each one over making sure they were in proper working order before setting them aside to be packed up later. Sarah wasn't quite sure why he was already doing this part when they didn't even have a solid plan yet.

"Casey, we don't even know what we're going to do yet, why are you pulling out weapons?" She asked him leaning against the table. He glanced at her for a second before snapping the magazine back into the 9mil he was checking.

"That thing may have taken over Bartowski but I'm sure as hell going to make sure he's covered." He growled out. Sarah just shook her head.

"I doubt he'll be able to even carry all this, let alone use it. Plus you know that Chuck doesn't like guns." She pointed out, picking out a few flash grenades.

"Chuck may not like guns but that thing isn't him. I'm sure that it has no problem taking a gun and shooting someone as you've seen. And it's not just for him. Do you honestly think you'll be able to stay in the car while Bartowski goes in there by himself? This is a suicide mission Walker." He stated as he grabbed a bag from underneath the gun rack.

Sarah wasn't quite sure what to say. She didn't agree it was a suicide mission, being as she doubted the government would send their new super-agent into one so soon after finally getting what they wanted. But she couldn't tell Casey that. She could tell by the way he clenched his jaw and slammed the weapons around that he was upset over this whole thing. She chose to ignore the comments about Chuck using actual guns for the moment.

"Ok, well, what do you propose we do then?" She asked him, trying to distract him and get into the planning. The best way to keep Chuck alive during this is to come up with the best course of action.

"The solution is simple. You two shall come with me." They turned around quickly at the voice behind them and saw Chuck standing there looking at them. Sarah's heart beat quicker at the start, cursing herself for not noticing his approach.

"You're to do this alone Bartowski, Directors orders." Casey growled, narrowing his eyes at the person in front of them.

"I understand the parameters of this mission well. However it is my assessment that if this mission is to be successful than I will require your assistance." He intoned.

Sarah looked towards Casey, hoping to see what he thought of this but as usually his face was a perfect mask of indifference. Her eyes met Chucks for and for a moment she thought she saw the softness that she was so familiar with but in a second it was gone.

"And the Director? This is a test. A test for you, to see how you perform in the field." Casey said returning to packing the weapons he'd pulled out into the duffle bag.

"The Director is of no concern in this. The point of the test is to see how I perform using the resources available to me. You two are available and therefore will be used." With that he placed the file that the Director had handed him onto the work table and opened it up, showing a map of the compound. "If you two enter here and I enter over here." He stated pointing to two separate entrances. "We shall be able to achieve the objective."

"Plant a little C4 down the corridor as we go along and exit out the southern exit, we could detonate and blow half the place up." Casey stated looking at the building plans.

"The Director wants as much of this cell eliminated as possible." Chuck stated looking up and over to Casey. "I suggest you bring the rocket launcher."

The look on Casey's face scared Sarah slightly. She had never seen such a huge smile on his face and she was frightened by it, and by the fact that Chuck had suggested it. Everything felt wrong. The plan felt wrong, the equipment felt wrong, Chuck felt wrong. Casey's near teary smile felt wrong. She couldn't take it anymore and had to get out of there.

"That's fine, its fine. Finish packing and we'll head over in an hour." She said quickly before walking away from the two of them.

She walked to the conference room and stood there a moment before sitting heavily into one of the chairs. She covered her face with her hands and took several deep breaths trying to calm her emotions. She didn't know why they were out of control at the moment, having been trained and able to hide them for years, but she couldn't let them get ahold of her.

That's not true; she knew exactly what was wrong. The same wrong that has been happening over the past three days. Since the Intersect first took over Chuck. She wished hard with all her might that she could just wake up and all this would be over or just a bad dream. That she would awaken with a start and find herself wrapped in Chuck's arms, safe and secure and that this had all been a nightmare.

"Agent Walker are you alright?" Chuck inquired stepping beside her. For a second time she jumped startled at not hearing his approach and looked up at him glaring.

"Since when did you become so quiet when you walk?" She bit out harshly, only to feel bad and want to take it back the next second. It wasn't his fault.

"I apologize Agent Walker." He said. "May I sit down?" He asked pulling the chair out and sitting without waiting for a reply.

They sat there in silence for several moments as Sarah observed him. Her heart ached as she watched him. It was barely twenty four hours ago he was still her Chuck. That she was in his arms and telling him how much she loved him. On the surface he looked the same, he hadn't changed. He had the same curly hair, the same long limbs, and the same soft looking lips that she wanted so badly to kiss.

But she knew he wasn't her Chuck. While outwardly they may look the same, the look in his eyes alone told her they were different. Instead of soft brown eyes that showed anybody who bothered to look his soul, they were hard and indifferent, calculating. His lanky body that was once limber and awkward, even after all these years now sat stiffly and in control. Everything about him shouted that he was not Chuck Bartowski, and the knowledge filled her eyes with tears she refused to let loose.

Sarah turned away from him, no longer able to look at the face of the man she loved more than anything. She couldn't stand to see the indifference he showed her, or the silence that held between them. Everything in her being shouted at her to just grab ahold of him, press her lips to his and kiss him for all she's worth. That just maybe one of those fairy tales that Morgan was always blabbering about could come true and fix this, but she held back, not sure what the machine inside her loves head would do if she let herself go.

"I know you care about Chuck Agent Walker." The Intersect told her. She scowled looking back at him, watching his human eyes calculate her. She had a retort but bit it back, not able to say it to him, to the face of Chuck. Instead her scowl turned softer and she looked back at the table.

"Please, call me Sarah." She said softly. She waited for a response of some kind but none came. She glanced up from the table, startled to see him staring at her unblinkingly. "You know, it's not polite to stare." She said lightly giving a small smile.

Sarah watched fascinated as the machine in front of her lifted Chuck's lips up in the corners to imitate her. It looked more like a grimace than a smile and it made her sad thinking she may never really see Chuck's smile again.

"I'm sorry. I haven't fully grasped all the functions of the human body." He stated lifting his hand in front of him and flexing his fingers. "It's quite a miraculous machine. Very complex-"

"And not yours." She bit out angrily before she could stop herself. She looked away from him and stared straight ahead not wanting to see if her words had any effect on him.

"I understand you are upset over Chuck." He said, lowering his hand back to the table as she turned to him incredulous.

"Upset? Is that what you call how I feel? You, a computer program took over my boyfriend, the man I love and was planning on spending the rest of my life with. You took him away. Trust me; upset does not begin to express how I feel." She shouted at him.

Sarah stood up and walked a few feet away from him, pausing for a second before turning back and stepping right into his personal space. She was well aware that he could easily take her out with barely any effort but she wasn't afraid of him. With Chuck gone she felt even more invincible since she felt she had nothing else to lose.

She stood above him staring down into his eyes contemplating her next words considering the wisdom in them. But she had to know, she had to be sure. She wasn't giving up yet but she wanted to hear it from the Intersect, from the thing that did this. She watched his eyes as the pupils dilated and glazing over as if in a flash for a second before focusing on her.

"Is he really gone?" She whispered to him, holding her breath. He seemed to watch her for a few moments, gaging her reaction to all of this, seemingly thinking before replying.

"I am sorry Sarah, Chuck is not available." He told her firmly. Sarah stared at him a few more moments before turning abruptly away from him and walking away without turning back. She didn't believe him, and somehow she would prove it. "Are we going to be able to rely on your Sarah Walker on this mission?"

Sarah stopped in her steps and stared straight ahead contemplating making some sarcastic remark or comment. But she didn't, reminding herself that she had to be the consummate spy, and that Casey also relied on her.

"I will do my job to the best of my abilities. That I can promise you that." She said before exiting the room.

A/N: There. I took the week or so off to figure out where i'm going with it and frankly i have no frickin clue. I still feel i'm over my head with this technical fighting stuff. so thanks for sticking with me.


	8. Chapter 8

A/N: Ah, another chapter. Guess its going to be a weekly thing. Disclaimer: I know nothing about guns, weapons, explosives, or fighting. Though i think i did a pretty good job if i say so myself :-d

Thanks of course to charahkids for making sure it makes a bit of sense.

Chapter 8

Apprehension once again filled Sarah as they approached the compound where the flash drive would be located. She wondered what was so important about this item but could not find any additional information about it either in the files they were given or by contacting the Director. For all she knew it was just a random flash drive that the CIA wanted them to acquire to test out their Intersect. She wouldn't put it past them to pull something like that.

She was also concerned about why the CIA had decided to put them on the team with Chuck. Knowing their past and her relationship with him it made no sense to her to put them all together even if it was meant to be an observation role. If it were her she would separate them as far as possible, or at put a hit out on them.

That thought caused her to pause in her step by the building. It was something that hedged on the edge of her mind but not something she could bring herself to think about. She was well aware that they could order Chuck to take out both her and Casey. And that thought alone put her senses on higher alert, glancing at Casey a second and wondering if he had thought about it as well.

She watched Chuck as he walked silently along the darkened outside wall of the building to the other side to enter the building from there. The way Casey and Chuck made it sound in their final briefing it was a simple in and out mission but Sarah knew better from experience that nothing is as simple as it seems.

There were too many unknowns involved like how many enemy agents were in the building or out. Wheather they had backup on the ready in case of an ambush. Or a scarier thought, was there some kind of self destruct on the building they were about to break into. Nothing was really known, not even the name of this group whoever they were that they were taking out. Just more nameless faces to be added to her long list that she's acrewed during her time in the CIA.

With that in mind she cautiously looked around once Chuck was in place before placing her foot on Casey's outstretched hand in order to get a lift into the window above that was slightly ajar. She pushed it up a little further so she could slip into the room easily before turning to open it the rest of the way for Casey.

She grabbed his arm and helped pull him up as he grunted at the effort before finally entering the room with a soft sigh.

"I hate to admit it but I may be getting old for this shit." He muttered to her as he stood up straight. Sarah had to turn her face away from him so he couldn't see her amused smile, not wanting to anger her partner. Thought it amused her she would never actually agree with him. As age catches up with him he was still quicker than anyone, even her at most times so she would keep him around for as long as she was able, which was to say, to the end.

The room was as dark as the last one she had broken into but unlike that one this place was slightly cleaner. It was obvious this room was used for something, but for what she couldn't tell in the dark. Sarah crept to the closed door on the opposite side of the room as Casey pulled his backpack off and began pulling out explosives.

She watched him for a moment, still not sure if this was the best thing. Casey had been right now that she thought about it, that this was a suicide mission for Chuck. She was glad that the Intersect was actually intelligent and not just something that blindly follows orders and thought to bring them in to assist.

Sarah felt a twinge of anxiety over the whole situation, something she had never really felt before she met Chuck. Before she would follow any order blindly with as little information needed and do whatever was needed to make the mission succeed. However ever since she met Chuck, and even more so after she admitted her feelings for him and begun this new life, she couldn't help but question more and more about what she's done or what she's doing.

She wasn't sure if she liked that change in her. Spies who think too much tend to get in a lot of trouble on missions, or worse dead. A spy has to be able to think on their feet and follow their instincts to complete their mission and get back alive. But now she couldn't help but stop and think about things, work them out before the mission. And worse she couldn't help but question her superior's motives on sending them out on missions.

It wasn't entirely a bad thing. She got a good trade off. While she questions things more and follows less blindly Chuck has given her more in her life than she ever thought possible. He gave her a future. Before she lived in the here and now, never thinking of what may come. She never thought she really had a future. While she didn't technically have a death wish it just wasn't something spies planned for, with their jobs being so dangerous and unknown.

But ever since she met Chuck and more when they began their relationship, he's opened her eyes to a whole different world. One where there aren't people around every corner trying to kill you, where there are good people in the world. Where there are families and friends that genuinely care about you and willing to do anything to help you or just plain love you. It scared her at the same time it thrilled her. For the first time in her life she saw her self having a life, a family, and she was in love.

At the moment however it seemed up in the air. With the government taking over Chuck her future was once again bleak and unknown. She knew she could never go back to the old Agent Walker, the one she was before she met Chuck. She had learned too much, felt to much, changed too much to do that. She wasn't sure what she will do, but for the moment she would just focus on the mission at hand.

As soon as Casey was done setting up the explosive in the room he walked quietly up behind her by the door and they counted silently to three before cracking it, pausing momentarily in case the door squeaked. When no sound came they opened the door more to peer down the hallway.

There were several guards walking up and down the corridor outside the room they were in. Dressed in green and carrying large guns, Casey and Sarah waited until they passed the room they were hiding in before quietly exiting and shooting them both in the back of the heads. Soft pht sounds coming from their silenced weapons were the only sounds heard as they dropped to the ground.

With the two guards taken care of they dragged their dead bodies into the room they had first entered in, closing the door silently before trailing down the hallway towards their destination. They only met a few more guards along the way, taking care of them and hiding the bodies in the rooms along the way. Casey took an extra moment at each stop to pull out another explosive, setting it to go off remotely.

Continuing down the hall they made a left at the junction at the end, not finding the office they needed on that side of the building. Casey and Sarah turned and headed further down to the other side when they heard a click of the safety of a gun being released and turned around quickly to shoot, luckily pausing before taking out the person behind them.

Chuck stood behind them, guns in both hands pointing at both of them. Sarahs heart beat wilder at seeing it, not liking how easily he held them in his hands and even more so how he easily pointed them in their direction. Taking a deep breath to quail her emotions she lowered her own weapon away from him and just stared.

"Chuck, you really need to stop sneaking up on us." She scolded looking over at him. Chuck didn't waiver in his stance or lowered his weapons, momentarily frightening Sarah. Looking over at Casey next to her she noted his same stance. Panic filled her at the glower that Casey gave Chuck, knowing full well that they were both capable of killing each other and though she wasn't there she was well aware that Chuck would have asked Casey to take him out in the event that Sarah couldn't. "Lower your gun Casey." She said quietly so only he could hear her but he ignored her, staring straight at Chuck.

Sarah didn't know what to do. Thoughts ran through her mind on if this was some kind of joke or if the Director really had ordered the Intersect to eliminate them, doing it on a mission so it couldn't be traced back to him as a hit. She knew without a doubt in her heart that Chuck would not be capable of fulfilling that order, but right now, the man, or thing in front of her was not her Chuck, and was fully capable of killing them.

The tension became too much for her after several minutes making the air around her stuffy and hard to breath and her head sped up. She took a step to intervene, not sure exactly what that would accomplish. She took a step forward towards Chuck first but stopped immediately as both his guns went off giving off single silent shots before he finally lowered them, pointing them to the ground.

Sarah paused, shocked as she watched him. She felt numb inside but still waited for the pain that would inevitably come from being shot but it never came. She felt her lungs burn as she let out the breath she had been holding in, but feeling no pain other then in her heart she looked down and saw she was fine before glancing at Casey who was looking behind them.

There on the ground were two more soldiers, blood pouring from the single bullet wound to the heads. Sarah stared at them in horror and feeling came back to her and her mind cleared as it came back to the present.

"We've lingered here long enough. The last rooms should be up ahead." Chuck stated, shouldering past them and walking further down the hall.

Sarah watched him alarmed, unsure of his actions. She really felt for a moment that he was aiming for them, but with the dead soldiers in front of her now he could have been aiming at them the whole time. She didn't know, and she wasn't sure what to think at the moment, but she decided to keep a closer eye on him and as much as she hated it, she would have to be more wary of him.

With a final glance at Casey, noting his expression conveying the same feelings she had, he gave her a quick nod indicating they should follow. They walked down the hall, checking out more rooms as they went, unsure if Chuck had done them himself since he was so far ahead. Casey paused in each room, taking explosives out as he had been doing and setting them up. Sarah had no doubt that there would be very little if anything left of this place left when they were done.

And they still had the rocket launchers in the van.

Finishing with the final room on the left they stood up to exit the door when a loud bang and shout echoed down the hallway, followed by a loud scream and several gun shots.

Sarah exited the room quickly and ran down the hall, turning the last corridor and opening the heavy double doors that stood at the end shoving them hard as something was behind them. Pushing them open the room opened up into a large warehouse area full of boxes and vehicles. Looking behind the door to see what had blocked the door, a large man laid still blood spilling all around him as it leaked out of his neck where his throat had been cut.

Not giving the time to feel sick at the gruesome sight Sarah turned around in time to see a man come up to her and swing his arm to punch her. Sarah ducked low turning to sweep his leg, grabbing his arm as he fell back and banging it hard into the doors knocking him out as another one jumped on her back causing her to fall to the floor

Bringing her elbow up on her free arm she hit him several times in the nose and face, using all her weight she pushed up forcing him off her and allowing her to get up and turn quickly to kick him in the face, blood splattering everywhere.

She was going after the next person who was running at her when the sound of guns going off caused her to stop and duck down behind the nearest cover and pull out her own weapon. Taking a second to get air back in her lungs she looked around the front of the SUV she was behind to see who it was that was shooting.

There standing in the middle of the room was Chuck. He had guns drawn and was shooting at random while physically taking out those closest to him. She stared in horror as he dropped his guns once out of ammo and pulled knives out of his side holsters.

She watched as he kicked out wrapping his ankle around the knee of the guy behind him and pulling in forcing him to fall before round house kicking him in the head knocking him out. Swinging his arm around a big burley man stopped him and twisted it hard causing a grimace on Chucks face. It didn't last long however as he kicked his knee up hitting the man in the stomach and plunging the knife in his other hand down hard into the side of the guys neck.

Sarah covered her mouth in horror as Chuck pulled the knife from his neck, blood pouring and shooting out as the man let go of Chucks arm and Chuck kicked him aside to fight the next guy. She was frozen in place unable to move, unable to help, unable to do anything but stare terrified at what that computer was making Chuck's body do.

"This is getting ugly." Casey's voice said behind her causing her to jump slightly. She berated herself silently for it happening yet again. This whole situation with Chuck was really affecting her spy skills and she wasn't liking that at all. If she didn't pull herself together soon she could be very much dead and she wouldn't have to worry about the CIA, or Chuck, or any thing else.

Casey pushed up over the top of the car and pointed his gun at some nearby enemies, shooting them down with deadly accuracy. Taking one more second to herself Sarah peered around the vehicles front and began shooting at the men who surrounded Chuck, changing the clip quickly and efficiently as needed.

She wasn't sure how long the shootout took, or who shot who exactly. All she knew what Casey was behind her blasting away while she tried to take out as many men who were after Chuck as possible before they reached him. Of course she couldn't get them all, and neither could Casey, so those who were lucky enough not to be killed by their bullets met their ends painfully and messily through Chuck's knives.

Finally the blasting stopped and all was silent except the ringing of her ears. Her vision was blurred slightly from the darkness of the warehouse like area and the dust that had settled up from all the activities. Sarah coughed a few times trying to clear the gunk from her lungs before slowly standing up and leaning tiredly against the hood the car.

"Chuck?" She shouted out amongst the debris, having lost sight of him not too long ago. She prayed he wasn't injured by either a stray bullet from them or one of the people who were after the three of them.

"Come on." Casey growled out moving away from the vehicle and over to where they had last seen Chuck.

Sarah stepped over the nearby bodies that had fallen near where she had taken cover, grimacing as the total began tallying up quickly, but she steeled herself, swallowing hard and brought the Agent to the front taking complete control.

They walked to the left side of the room, where Chuck had last been and looked around at the chaos around. Bodies littered everywhere lying in a large pool of blood that were mixing from the many wounds of those who were piled up dead or dying in the area. Sarah covered her mouth hiding the shock of the twisted forms that piled upon each other, eyes widened horrified at seeing someone still alive at the bottom trying to push his way up, moaning in such agony.

She stepped forward, over a few more bodies to reach out the help but stopped at the sudden blast that came from behind her and she watched as the body stilled for the final time. Looking behind her she saw Casey holding his gun out at the man, smoke still lingering from the barrel.

"Orders were nobody left alive Walker." He said simply lowering his weapon. Sarah closed her eyes for a second before opening them up and heading away in the opposite way, still looking for Chuck.

She walked around to the opposite side and opened the double doors that were there cautiously, well aware that there could be more enemies about. Seeing nothing in the darkened corridor she slipped in silently, gun drawn and began making her way slowly down the hallway.

She knew she was on the right track, bodies littered the floor as she walked leaving a trail of where Chuck had gone in his wake. He must have been confident the only ones who would be looking for him would be on his side to leave such a mess. Hitting the end of the hall she sidled up against it and peered around the corner, seeing a small hall and a single door at the end that was closed. Drawing her gun closer to her body she crept along down the short way till she reached the door. She tentatively put her hand on the knob, getting ready to turn it when the door was swung open.

She gasped as she was startled at the sudden appearance of Chuck, both spies in front of each other with weapons drawn. Her eyes were wide as she stared up at him, noting his calm aura despite his disheveled bloodied appearance. Her breath hitched at seeing him covered in so much dirt, grime, and worse mystery blood from the victims of their assault.

They stared at each other for several minutes, no sounds passing by them as they stood in their own world where only the two of them existed. If she looked hard enough Sarah could have sworn that she saw her Chuck's eyes glint at her in recognition. Light up for a second as they used to whenever he saw her. But it was gone the next second and her heart fell, chopping it down to a trick of the light.

"Imagine that." Chuck said softly, not lowering his weapon from where it aimed between her eyes. "Here in the darkened hallway with nobody around." She narrowed her eyes at him, confused by his words.

"I don't understand." She stated firmly, lowering her own gun only slightly. She hated pointing it at Chuck but something in her gut told her to not give in and relax around him. That he may look like her Chuck but he is anything but. He was dangerous, and unpredictable.

The corners of Chuck's mouth curled up in a smirk, causing her to want to throw up. She hated smirkers and she hated that look on Chuck. Agent Walker screamed in her head at Sarah to end it, to walk away and get out of there and away from him, to call for Casey, to do something other than stand there.

"Here, with no witnesses, you could end it you know." He told her calmly, finally lowering his weapon and opening his arms as if inviting her to step into his embrace or welcome a bullet from her gun. She watched him warily, the smirk never leaving his face.

"I don't know what you are talking about." She said quietly, not taking her eyes off him. Chuck let his arms fall to his side casually and watched her. Sarah felt sweat begin beading on her brow as she stood under his scrutiny, but she refused to show any weakness in front of him.

"You don't have to lie to me Agent Walker. I know what he asked you for. I know of his request." He told her plainly.

Sarah's gun lowered, expression going from impassive to surprised, though why she was she didn't know. She knew the Intersect was in full working order by that time, so of course it would have known about that conversation with Chuck.

"Is that what you want? To end it?" She asked, not bothering to pretend to not know what he was talking about. The Intersect didn't reply, just stood there staring back at her, stance relaxed, not caring that a trained assassin had a loaded weapon aimed at him.

The tension between them grew at a staggering rate until Sarah found it difficult to breath. Standing there watching him, she felt the full weight of her gun as she met his gaze. He was right, now would be the perfect time. There would be an inquiry of course but no one would really question it. Would really believe that she, Sarah Walker would take out Chuck Bartowski, her loving boyfriend.

She raised her gun more firmly, snapping Sarah Walker away and allowing Agent Walker to take front and center. She aimed the gun right up at him, right between the eyes. She could do it now and make it quick, make sure Chuck would never suffer. End it all right now.

But then she inhaled, filling her lungs with air getting ready to fire but failed.

She couldn't do it. She couldn't kill Chuck, even if he was really gone. At least not yet. It was why she told him only when she was sure there was no way to save him. She knew that if it came down to finally doing the deed that she would have to be prepared for it. She would have to ready herself for it and even then she'd probably end up taking herself out at the same time.

She hoped Casey would do it.

Sarah dropped her arm and stepped back looking away from Chuck. She felt tired and drained as everything came crashing back onto her. She felt the full force of everything they've done today, and all the stress she'd been under for the last couple days. She felt her eyes burn as tears threatened to come, but she would at least hold that back. She refused to cry right now in front of this machine.

Chuck hadn't said anything else during the whole exchange, just watching her carefully, as if knowing exactly how she would react, what she would do. She hated that he could do that, know her so completely when she didn't know anything about it. She raised her hand and brushed a strand of hair that fell out of her pony tail off her face and sucked in some air before finally turning toward him.

"Lucky for you I can't do it." She said quietly. "But you knew that didn't you."

Chuck shook his head slightly before turning around and entering the room. Sarah took that moment to look around it for the first time since the door opened, noticing it was a small office. Paper was laying all over the place as Chuck ransacked it looking for the flash drive they were sent there to collect.

"I was warned that you might try, but I knew you wouldn't." He told her opening the desk drawer before looking back over at her. "Yet." Sarah walked into the room and stood in front of the desk with her arms folded over her chest.

"And you? If they thought I was so much of a threat for you then why didn't they order you to take me out then. Now would have been the perfect time, for Casey as well." She stated watching him as he closed the drawer he was looking through and opened it for another.

"Is that what you want Agent Walker? To be taken out of the equation?" He asked her not pausing in his search. Sarah thought about it for a moment and it frightened her that her immediate answer was 'yes'. If she couldn't be with Chuck she didn't really have much left, and that thought scared her. That she became one of 'those' girls and she was slightly disgusted with herself. But she had lived a life of hell since birth and for the first time in her life she felt alive. She would be able to survive without him, but she didn't know how much of her would be left now that she's seen the beauty the world can offer her.

"Obviously what I want doesn't matter, else you wouldn't be here." She bit back turning away from him again. The only sound in the room was from things being moved around in drawers before a final slam of the last drawer being closed startled her. She turned around and saw him standing there holding the flash drive out to her. Gingerly she took it from him and placed it securely in her pocket.

"We could be great you know. Partners in this." He stated simply. But Sarah shook her head and started walking away.

"I don't need another partner. I already had the best there was." She stopped and turned around at the door. "And you took one of them away." With that she turned around once more and exited, leaving Chuck staring at her back as she did.

She walked briskly down the hall and back into the warehouse area where she spotted Casey leaning against the SUV they had used for shelter earlier, a cigar hanging from his lips as he played with some mechanical device. She stopped a few feet away from him and placed her hands on her hips.

"Is that really wise to be doing that in here. You don't know what's kept in here." She questioned narrowing her eyes. Casey just gave her a quick smirk and a shrug before taking out the cigar.

"Does it matter Walker? Either way this place goes, whether we're in it or not." He stated simply. And he was right. She didn't want to die but if they all went up right now she wouldn't be disappointed. She'd be with Chuck and that thing wouldn't be able to use him anymore. But she shook her head instead shaking those dark thoughts from her mind.

"Chuck found the flash drive so let's go." She said walking away towards the back of the area where doors to the outside led.

She didn't bother to see if Casey followed or even if Chuck had come out of the office she had left him in. She just continued walking, gun drawn once again but not seeing anyone else around figuring any of those who had managed to survive was long gone. Either way she was cautious as she made her way off the compound and back to the van they had hidden away up on a hill out of sight.

They reached the van and Casey opened the back of it pulling out one of the rocket launchers and handing it over to Chuck before offering the other one to her. She declined it allowing him the honor as she knew he loved blowing shit up.

Facing the building she watched as Casey flipped a switch and waited till she heard the explosions begin from the inside of the building, covering her ears at the sounds of the rockets as they flew towards the air towards their destination and watched as they hit their target and exploded.

Sarah watched it with watery eyes, feeling she knew exactly how that building would have felt if it could. Feeling like everything it knew and held was being shot to hell.

With a final look and shove from Casey, Sarah got into the van and drove off.

A/N: So has anyone read the stuff from shortpinoyguy? His stories sound amazeballs but most of them are in script format so i'm just curious are they all intergated? like one hugeass series or can i pop into one and read it and be fine? Just askin, I can't read script format.

Oh! and i think i found out (finally) how to respond better to reviews! YAY! Cause i really love that people take the time to tell me how they feel about my writing. Thank you all who have reviewed!


	9. Chapter 9

A/N: Thank you to **Doc2or, Jimmy144, sevenrez, uplink2, johnmurray2, phathead01** for your reviews! I appreciate that you took your time to read and reply. Hoe you enjoy the next chapter. And I just want a special thanks to **wifi21** who reviews almost if not all my chapters and is very encouraging and honest.

Thank you to charahkids, my fabulous beta.

And I should warn you that there is a non-graphic shower scene in here. I realized my error in writing it but i'm too lazy to change it so suck it up. or skip through it :)

Chapter 9

She was exhausted, both physically and emotionally. She wanted nothing more than to go home, back to the apartment that she shared with Chuck and Morgan and to take a shower before curing into bed against Chuck and let the day seep away from her.

Well, at least Sarah could do a couple of those things. The cuddling part, she wouldn't be able cuddling part, she wouldn't be able to. Sure the Intersect may be Chuck in physical form but he is anyone but Chuck.

Once the mission was over they went back to Castle where Casey took the flash drive and the van to begin closing down the op. He told them both with his typical Casey grunt to go ahead and take off, get cleaned up and they'd meet again the next morning to fully brief the General and Director.

She watched as Chuck stood there staring at the menu in the Orange Orange looking lost and unsure, something she didn't think the Intersect could actually feel or know. Stepping up to him she had followed his gaze up to the menu, staring at the strange flavors listed before turning back to him.

"What's wrong?" She asked her voice hoarse from the night's actives. Debris, shouting, the smoke from the weapons; none of it was actually good for a person. Chuck stood there a few more moments before he lowered his gaze down to the counter.

"I'm unsure of where to go." He said simply, almost sadly causing a slight twinge in Sarah's heart. She didn't like the lost look that covered his features.

"Where would you want to go?" She asked him after a few moments pause. Chuck seemed to think about it for a few minutes before finally responding, still with a faraway look.

"Chuck would go home, to Echo Park. Clean up, relax. Play one of those video games with his friend Morgan to unwind." He said. Chuck turned towards her and her breath hitched at seeing sadness in his eyes. "But I am not Chuck, as you have pointed out. I am the Intersect. I have no place but where I am ordered to be."

Sarah stared up at him pensively, taking her time to note the changes in him, comparing them to her Chuck. He looked so sad and so lost, a look she'd seen on Chuck many times especially in the first few years when they weren't allowed to be together. When he was thrown into this crazy spy world far out of his depth and floundered at everything.

She didn't like it then and she didn't like it now. Especially now, knowing that the thing behind the look was not Chuck himself but a computer program forced into him. Sarah shook her head, clearing her thoughts. Her mind couldn't help but keep drawing the parallels and differences between them. She knew she needed to stop and treat this thing like he was Chuck and start acting like what it was, a machine, a parasite. Something that forced its way violently into the body of its host against the hosts will.

Looking back up at Chuck a minute later seeing him stare off to the side blankly made up her mind for her. She couldn't treat him like any other unwanted agent or creature. He wasn't like every other enemy. He was still in the man that she loved more than anything.

Grabbing his hand tentatively she took a deep breath before tugging his arm and pulling him out the door of the Orange Orange and toward her car. She was thankful for him following easily and quietly, not asking any questions, not making any comments. Just silence as he opened the passenger side door and got in. Sarah had to take a few moments to herself to get her wits about her before she too followed through.

The drive to the apartment was silent as Sarah gripped the wheel tightly. She hopped that Morgan would be elsewhere that night so she wouldn't have to answer any questions and deal with the awkwardness of the two best friends. She was thankful to Ellie when she offered to tell Morgan the bad news and explain their plan to him, not sure if she could have dealt with Morgan's inevitable crying as he lamented the loss of his friend.

Pulling up to her normal parking spot at the apartment she turned off the engine and leaned back in her chair and stared at the gate. She wasn't sure how she felt about this, bringing this machine to her home that she shared with Chuck, she almost felt like she was cheating on the man she loved. But to anyone else not in the know, to the outside world, the thing sitting next to her was Chuck Irving Bartowski, nerd extraordinaire.

"It almost feels like home, just seeing it." Chuck's voice raising softly, breaking her out of her own thoughts. She glanced over at him and watched as he looked all around him. Huffing out a breath Sarah unbuckled her seat belt and opened the door.

"Yeah well just remember it's not your home. It's Chucks." With that she got out of the car, shutting the door much harder than she would have liked or let anyone else get away with and walked up through the gate.

Chuck followed at a slower pace taking everything in. She could feel his presence behind her and she was grateful that he wasn't all on top of her at the moment, giving her some space. Sarah glanced across the courtyard over the fountain as she walked directly to her own door. The curtains were drawn but she could see some lights were on at Ellies place. She wondered idly if she should go over there now, get it over with. The introduction of this Chuck to his sister, but she shook her head against it. Now was not the time.

She unlocked the door to the apartment and dropped her keys in the bowl next to the door. It was something that the others sans her and Casey did when entering the door, making sure they could quickly find their keys again when needed next. She thought it was crazy but three years of being with Chuck and trying to act normal had caused her to start that habit to.

The light in the kitchen was on, as it always was when nobody was home. That was a habit Sarah herself imposed on the two nerds that co-inhabited the apartment. They lamented at the electric bill but she pointed out that it was a consequence of living with a spy. That and the 30ft gun rule. It made being snuck up on and invaded at night more difficult if one could see their surroundings looking for things out of place or even just the large man standing by the door with a knife or gun.

She walked in to the living room, stopping in the middle of it to do her cursory glance around the room. Seeing nothing out of order, noting the most like Morgan hadn't been home since she last left she placed her gun on the table behind the couch next to the game controllers that were kept there and finally looked over at Chuck.

The door was closed, causing Sarah to narrow her brow slightly at not remembering hearing it shut as she watched him. He looked around the room with that same lost look he had on his face when they were at the Orange Orange only this time it was more calculating, analyzing his surroundings.

"What is it?" She asked him, crossing her arms over her chest as she sat on the arm of the sofa. Chuck looked around a moment more before turning towards her, eyes still saddened.

"I remember this. All of this. It's so familiar yet it's so new." He said simply and turned away again, walking towards the entertainment center. Sarah watched him cautiously as he reached his hands out and gently touched everything there. Gracefully touching the equipment, carefully picking up a framed photo that sat on the shelf and stared at it.

"I'm going to take a shower." Sarah announced getting up from the couch and walking toward the hall. "His clothes are in the bedroom, you should know where." She said.

She walked quickly down the hallway, by passing the bedroom and going straight to the bathroom. Entering the room she closed the door behind her and leaned against it. She covered her mouth with her right hand and shut her eyes as tight as possible as she fought to breath.

She berated herself for bringing him here, into this place that had become sacred to her without her knowing. He was out there in their apartment touching Chuck's things, playing his life, while he was trapped someplace in his own mind held against his will.

Sarah let out a few shallow breaths and opened her eyes, tipping her head back to stare at the celling, blinking away the tears that were falling from them. Now was not the time. She didn't think there ever will be a time, but that didn't matter at the moment.

One more breath later and she pushed herself away from the door, bringing her hands up to wipe the stray tears that managed to escape their cage. She turned on the shower, making the water hotter than she normally liked it but needing to feel the scalding heat on her skin was more important at the moment.

Stepping up to the mirror she stared at her reflection as steam began to surround her. She looked the same as she always did. Pretty beyond most and professional. If it wasn't for the fact that she was the one who were feeling the emotions she would never suspect that the person staring back at her in the mirror was going through any turmoil. That the person she was seeing wasn't in pain and feeling loss.

Unable to stare at her own face any longer she turned away and lifted her shirt over her head and tossing it into the basket by the door. It was grimy and dirty with blood and would need special cleaning before she wore it again. She did the same with her pants, kicking her shoes off harder than necessary before finally removing the rest and stepping into the shower.

The water was hot, very hot and her skin felt it scalding it, turning it red and angry but not hot enough to actually burn. She closed her eyes and let the steam fill her sinuses as she let her mind drift off not thinking of anything in particular. It felt good and wonderful and for the first time in days she felt her body begin to relax.

"You are beautiful." A soft voice whispered in her ear and Sarah smiled feeling a blush rise from her neck to her cheeks as she breathed out Chucks name into the steam. She kept her eyes closed not wanting to break the vision that her mind had created, not wanting to leave her Chuck.

Her mind created a vision beautifully painted for her in her eyes of the two of them together. Of the many times they had spent time together in this very spot, in the same manner as she was in right now. Eyes closed with hot water pouring down on them and steam fogging everything around them, blocking out the world and its problems.

Sarah smiled as her mind brought forth the memory of the first time they made love in the shower together. She didn't think it was a possible feat. Being upright, water everywhere, soap, slippery skin. It was more of a skill challenge than anything but somehow Chuck made her feel as if she were in heaven and lying on their bed together.

She felt her skin tingle as something soft like lips trailed the side of her neck. Her heart ached and wanted to cry out to her mind, asking it why it would be so cruel as to conjure up such a realistic feeling. That is until she felt long arms wrap around her waist, pulling her towards a hard body tightly.

Sarah's eyes widened shocked and pushed hard away from the person who was holding her. Turning around quickly arm raised to take out who it was, but her fist was stopped in midair by a gentle fist that held it tightly.

Looking up she pulled her arm back as she backed up against the far end of the shower stall and tried to cover herself up and get her heart to settle. He mind was wheeling and her heart was aching and suddenly the comforting steam from a few moments ago was suffocating her.

"What are you doing here?" She growled out angrily, finally finding her voice. Staring at her alarmed, she saw Chuck stand near the opposite side of her and watch her with wide eyes.

"I'm taking a shower." He said as if it's the most obvious thing in the world. He opened his arms then giving her a full head to toe view of his nude body and it just made her ache more, but she stood steadfast against the wall behind the falling water.

"You could have waited until I was done." She stated still angry as she tried in vain to cover up more of herself. Chuck took a step towards her, lowering his arms slightly and she stepped back harder against the wall feeling the shower dials push painfully into her back.

"Stay away from me." She cried out, hating how her voice seemed to crack and sound pleading. But this was too much for her and she wanted to just get out of the shower and away from him.

"You don't mean that." He said calmly, but she shook her head.

"Yes, I do, stay away." She said. Ignoring her pleads Chuck reached out and placed his hands on her arms gently almost reverently and slid them up and down in a soothing manner. She hated how his touch felt so good, making her skin tingle amongst other parts.

She had nowhere to go, nowhere to run to. Chuck blocked her exit and the wall was already flat against her as much as possible. She knew she could take him out but she wasn't sure she had the will power to right now. She just wanted Chuck; she wanted everything to go back to how it was.

She closed her eyes tightly, hoping that maybe if she ignored him he'd get the hint and go away. She tried to release her mind, to not focus on what was going on at the moment that Chuck wasn't standing in front of her, touching her arms in the shower, naked and waiting for her to just give in.

Her brows narrowed over her closed eyes as she felt him lean closer to her and place a gentle kiss on her lips. It felt so good. She pulled away, pushing hard on his chest but he grabbed her hand in his, holding it tightly as he pressed on.

She felt his tongue lick her bottom lip begging for entrance into her mouth and it took all her will power to reject him, but it didn't last long. It felt so good, it felt normal. She gave in, parting her lips to his eager tongue, tasting every part of him as she finally let go of the wall and wrapped her arms tightly around his neck, pushing her body fully into his.

She felt his arms wrap around her waist and lift her slight up to better access her lips. She felt tingly and aroused as he placed gentled kisses along her jaw and neck before finally placing his lips back on her and kissing her for all he was worth. It wasn't until he raised her further against the wall and about to enter her that her senses came jarring back to the present at full force.

"Stop, no stop." She said out of breath and she started pushing him away with more force. When he continued she shouted. "Chuck STOP!"

Startled he took a step away from her causing her to fall back down to the floor. She held on to the wall, pushing herself into the corner behind the spout again as her legs shook. Her breath was panting as she looked up at him, his eyes saddened and confused again. Just like Chucks. Shaking her head away from the train of thought she pushed him aside and exited the shower, not caring about spilling water everywhere.

"Sarah." He said behind her as she wrapped a towel around her body, trying to hide it and herself. She didn't turn around, couldn't face him. "I'm sorry." He said simply. Not acknowledging his words she just opened the bathroom door quickly and ran into the bedroom, slamming it shut behind her.

Finally everything caught up with her as all the emotions that she had been holding back since this began came flooding into her body all at once. She felt herself go weak as her body shook in pain as the turmoil burned through her veins. She felt she was going to get sick if she stood up much longer and allowed herself to fall flat on the bed not caring that she was soaking the blankets with her wet body.

Finally she allowed the tears to fall, let the pain in her chest come out as she sobbed until her throat hurt and her body shook. This wasn't the way it was supposed to be, she thought. They were supposed to have their happily ever after. But yet again the government fucked them over and took it away.

She sobbed for them, for Ellie and Devon losing a brother. For Morgan and Casey losing a friend. But most of all she sobbed for the, Chuck and Sarah. For all the dreams she'd allowed herself to dream, for all the promises he made to her that he was inadvertently breaking. For everything they would miss together, adventures and lives as both a spy team and a couple.

She wasn't sure how long she laid there on the bed. 'Chuck's side.' Her mind supplied unhelpfully. Eventually the sobbing subsided and the tears stopped falling, and all the energy she had left was to lay there on her side, head on Chuck's pillow inhaling his scent and staring at the photo on her nightstand of the couple together.

It wasn't until she heard a faint buzzing coming from behind her that she finally got her senses back. Covering her eyes for a few seconds she uncurled her body that she hadn't noticed was wrapped so tight in a ball and turned to pick up the phone she had dropped on top of a video game magazine of Chucks.

It was a simple text message from Ellie asking how the mission had gone. She had forgotten that she had told her of the task that the CIA had put on Chuck that night. Was it that night? She couldn't remember. Everything was beginning to blur together into one long day of pain, misery and confusion.

Deciding that she couldn't stay there any longer that night Sarah sent a quick text back asking if she could come over and waited patiently for Ellies text back stating that of course she could. Relief filled Sarah's body, at remembering that she was not alone with this. That unlike her many years as a spy before the Intersect, Sarah now had friends and family to help her through this.

It took her longer than it should have to get dressed. Typically she would have just thrown on Chuck sweat pants and a shirt, not caring exactly how she looked. She had learned to be herself and not have to always be put together around family. But one glance in the mirror brought the ache back in her chest so she changed into her own clothes.

Sarah must have looked worse than she originally thought when she looked in the mirror before heading across the courtyard. As she opened the door Ellie immediately went into big sister best friend mode and brought her into a tight squeeze of a hug before bringing her inside to the couch where tea was already sitting for them.

"Where's Devon?" Sarah asked curiously, looking around the room, taking the moment to do so to compose herself. She wasn't prepared that Ellie's concerned reaction would cause more emotions in her to come up.

"He's at the hospital. Don't worry Sarah." Ellie told her, obviously knowing how Sarah would feel appearing to be weak in front of others. "How did the mission go?" She asked Sarah.

"Mission accomplished." Sarah replied simply, bringing her leg underneath her on the couch. "It went smoothly. Chuck performed, perfectly. The CIA will be proud." She could tell by Ellies grimace that she had said that more harshly than she intended.

"Did he, you know?" Ellie asked her vaguely. But Sarah knew what she was asking.

"Yeah. Oh yeah. And when he ran out of bullets he went in with knives. It was very…gruesome." She said looking away and more tears came to the forefront. Ellie covered her mouth, eyes wide for a few moments as she no doubt tried to picture it in her mind before shaking her head horrified.

"I can't even picture Chuck with guns let alone killing people. I just-"

"Well its true. If you had been outside an hour ago you would have seen the results of it. Him covered in grime, dirt, blood-"She closed her eyes unable to finish as she thought about the shower. She couldn't believe how badly she wanted it, wanted him. It had barley been twenty-four hours and she was ready to bop that thing.

"I know Sarah. I'm sorry." Ellie reached out for Sarah's hand and squeezed it comfortingly. "I'm just finding it so hard to deal with, and I haven't even seen him yet. But you, you've witnessed the change first hand. I can't even imagine how you're coping."

'Not very well' Sarah said to herself.

"Honestly, I don't think I am." She admitted softly. She wasn't sure if it was loud enough for Ellie to hear but the second squeeze around her fingers confirmed it.

"I think you're doing great so far Sarah. This is a hard situation." Sarah laughed lightly at that wondering what Ellie saw that she didn't.

"Before you texted me I was laying on the bed in a towel crying my eyes out." Sarah paused a second looking directly at Ellie. "I don't think I'm doing as well as you think."

"Don't say that Sarah. So you cried a bit? Its natural. Your emotions are all over the place and crying is a way to get them out. Now that you had your little sob session, maybe now you can focus more on the task at hand." Ellie suggested encouragingly.

Sarah hated to admit it but Ellie was probably right. She was a doctor after all. She had been having trouble the whole time because of her emotions and maybe now that she got them out she'll be able to get herself more together so she can do what needs to be done. Whether it's getting Chuck back, of fulfilling his request.

She still wasn't sure how she would do it. It was hard enough as it was and she was so confused about Chuck and the Intersect. One second he was the program the next he was like her Chuck. But she knew it wasn't him, Chuck wasn't the one in control or ever there.

"Ellie, I-"She paused, not sure how to explain what she wanted to say. "Chuck, this Intersect-"

"It's ok Sarah, tell me." She encouraged scooting closer to Sarah. "Any information you have even from observation can help." Sarah wasn't so sure.

"It's just that, sometimes, the Intersect, in Chuck acts so, human like." She spat out, internally rolling her eyes at how lame that sounded. But Ellie was watching her with rapt attention. "Like in the shower-"

"Wait the shower?" Ellies eyes widened alarmed scanning Sarah. "Did he hurt you?"

"No no, he stopped, when I said." She assured her, seeing her relax a bit in relief. "But the way he kissed me, and touched me. The way he interacts with me, us, Casey too. It's just; I thought that with it being a program that it would be more…" She couldn't think of the word but apparently Ellie got the drift.

"You thought it would be more mechanical. Like a robot." Ellie finished for her.

"Yes! Exactly. But it's different. I mean, it's obviously not Chuck but if I was any other person, I wouldn't know that it was a program." Sarah blurted. She watched Ellie intensely as she analyzed what Sarah was saying. It was one thing she hated about the Bartowski's. They thought, A LOT. Before sharing.

Finally Ellie sighed and changed positions on the couch, grabbing her tea and taking a sip of the hot liquid before speaking.

"When you told me about this yesterday you brought up a theory, that the program might still have Chuck. That it would have called you Agent Walker and not Sarah." Sarah remembered, both frightened and hopeful at the theory. "Well, you could be right or it could be something else."

"Like what?" Sarah asked confused.

"That thing has been in Chuck for several weeks Sarah. It's been learning from him, remember? What the world knows about AI in just about nothing. Everything we know is speculative from sci-fi TV. It's human like qualities could just be a result of that. Of learning from Chuck and now being in its environment."

Sarah thought about that and knew Ellie was right. She knew nothing about AI's and how programs work. She was thinking of it as any other computer program that Chuck's messed with or told her about. But there was so much she didn't know about it, like apparently it can learn.

"But it says it remembers. He said our apartment felt familiar." She said almost pleadingly. Ellie gave her a sad look and Sarah knew she was being pathetic, but she didn't care at the moment.

"He has Chuck's memories. That I know Sarah." She said. "I may not know much about all this but I'm very confident that there is no way to completely wipe out a human. Something would remain and it would most likely be memories."

Sarah stood up and walked a few feet away looking out the window across the darkened courtyard. She could see Chuck standing in the kitchen doing something, probably making something to eat. She shuddered as she remembered the shower once more and how good it felt but she shook her head to knock it away from her thoughts.

Feeling exhausted suddenly, though really it was no surprise she turned towards Ellie again. The older woman sat on the couch watching her with warm concern. Ellie opened her arms to Sarah and immediately Sarah collapsed back onto the couch and into her embrace inhaling the scent of soap and a light perfume that was Ellie.

Yet another testament to how much Sarah had changed. How much Chuck had changed her. She would never seek physical comfort from others when in pain but this felt good and she felt her emotions bubble up to the top again.

"Can I stay here tonight?" Sarah asked, feeling she couldn't handle facing Chuck again that night. Ellie held her closer and placed a soft kiss on her temple.

"Of course sweetie, you're welcome any time you know that. Do you want me to send Devon over to watch my brother?" She asked. Sarah shook her head and reached for her phone to call Casey.

"No, it's ok. We still have the surveillance up. Casey just has to turn it on." She replied sitting up again, she was in the process of dialing when she saw Ellies expression.

"Yeah, you know that is never going to not be creepy." She told Sarah, causing them both to laugh.

It felt good to laugh, even for a moment.

A/N: Again i apologize. I'll keep the future chapters cleaner. See you next week and hope your day goes well!

Missy


	10. Chapter 10

A/N: Thank you my dear friend **charahkids** for being my beta. Thank you **goddesslars, gcg23, doc2or, wilfi21, sevenrez, uplink2, shutupnkissme313, jimmy 144, Normadic Nerd, mrbi11, nerdtastic78, **for your reviews.

This is a little throw away chapter. I needed to get from one place to another so here it is. Enjoy!

Chapter 10

Two days later Casey sat in a mostly empty bar a few miles away from the Buy More waiting for Sarah to show up. They had decided they had to meet to discuss the situation but was unsure about what kind of surveillance they were under.

He was fairly certain that his apartment was fine, being as he searched for bugs every other day as well as having the best security system available and anti-surveillance equipment always running. However Sarah was still too paranoid, being so close to Chuck in the next apartment to speak there.

He didn't really blame her. What they had to discuss was considered treason and the less people who know about it the better.

He glanced around at the bar, taking in the dark atmosphere and the patrons that were around him. It was a little run down place he had discovered on a previous mission in California, before the Intersect project. He had needed a place to eat that was low key and the whisky while cheap was as good as the food they had served. He was left alone to his own devices without all the annoying chit chat from those around him or flirting from the waitress.

The only patrons around were at the bar, watching the one television screen the joint had with some football game on it. Casey gave a silent snort. It always shocked people when they tried connecting with him over sports to find out he didn't watch them. It was one of the few things he shared with Chuck was that people made assumptions on him based off his appearance. They see a big muscly guy they think sports nut. They see a scrawny nerd they think, well, nerd. Though they were right mostly on that.

What they didn't see was the brave geek that put others before himself. That was pushed into something he had no business and no will to do in the first place and succeeded well beyond what was ever expected. That he had more integrity in one little nerdish toe than most people hand in their entire bodies. That's what they didn't see.

Casey took another slow sip of his whisky and sat back further in the booth and let his head bump the back of it. He was tired. Something he would never admit to anyone. The mission had gone smooth but it felt like it was so trying. Though he was excited to finally blow something up again. It's been so long. On top of all the uncertainty that ran through his mind since this all began he also did surveillance at night on Chuck.

He was surprised two nights ago when he got the call from Walker to turn on the equipment, figuring that she would stay with him. However something happened, something that he still didn't know about and wasn't quite sure he wanted to and she had been staying at Ellies place the past three nights.

He lifted his head and he thought yet again about how screwed up the whole situation was. Everything was a disaster and Casey had a feeling that the shit hasn't even hit the fan yet. They were no closer to coming up with a way to save Chuck as they were when this first began. They had no plan, no course of action. Nothing. All they had was the damn CIA playing doctor on their friend.

A stream of light and the noise from outside increased slightly for a second as someone opened the door. Casey looked up from where he was staring at the table and nodded at Sarah as she entered and walked over to where he was, pausing to glance around the place cautiously before sliding into the booth across from him.

"Nice place." She commented off handily watching the patrons who had taken notice of the beautiful blonde who had entered the bar. He smirked a second seeing the deadly glare she shot out at them telling them one thing 'stay away'.

A middle aged waitress stepped out from behind the counter with the plate of fries he ordered and dropped them on the table. She looked over at Sarah, breaking her eye line from the other men taking her drink order. They waited for the waitress to drop it off before starting any sort of conversation.

"Fry?" He offered, pushing the plate toward her, but she ignored it, instead playing with the paper on the bottle of beer she had ordered. He thought it odd that she would order that, seeming more like a wine girl then beer.

"I don't know what to do." She said quietly, jumping right into it. Casey was glad for it, not being one for small talk but he didn't really want to discuss it. Emotions really weren't his thing. Taking another swig of his whiskey he watched her a little bit longer before replying.

"Well we have to figure it out soon. He's not going to be in our grasp for much longer." He stated, and it was the truth. The CIA Director had, despite the success of the last mission, assigned Chuck another one sans them. Something he didn't feel very confident about. He only hoped that whatever mission they were sending Chuck on it was actually something worthwhile.

Casey had always been the utmost professional, following orders to the letter. However finding out the next day that the flash drive they had been sent to retrieve was useless had pissed him off enough to break his silent stance and lay into the director. Only stopping when reprimanded by the General. The only comfort he had was that she too looked pissed off at what they were asked to do.

Sarah was horrified and silent, something he didn't think she could be when it came to Chuck. But hearing that they, or more specifically, Chuck had killed all those people for a flash drive that the Director didn't even know existed. The man actually laughed, hysterical that they had actually produced a flash drive.

Casey didn't feel guilt or anything for the men he killed, or for blowing up the compound. He had seen what they had hidden in those boxes when Sarah went off after Chuck. They had done a service to the country taking them out before they had a chance to do anything damaging. However Sarah didn't see it that way and there was no way he could or would convince her otherwise, because he sort of felt the same.

The kid was not a killer. He didn't like seeing him with a gun any more than he presumed Sarah did. He was just as horrified as she was when seeing him kill all those enemy agents, seeing him at the end of it covered practically from head to toe in their blood. Watching him as he casually took the rocket launcher from Casey as if he'd done it many times and launched it to the building below. It was a vision he didn't think he would ever get used to and hoped he wouldn't have to try.

"Have you been able to find out what he is doing?" Sarah asked, breaking him out of his thoughts. He shook his head, drinking the last of his whisky and setting the glass aside.

"No. I attempted to inquire with the General and she told me it was classified. Nobody knows. Whatever it is, its top secret at the highest level.

"I don't like this Casey. They're trying to split us up. They gave us our orders and we were still a team. And now they're splitting us up?" Casey nodded his head. He agreed with her, completely. But he knew how these people worked and he wasn't nearly as surprised as she was.

"My guess is the Director isn't too happy that Bartowski included us last time. He wants to see how the Intersect performs without interference or assistance from others." He told her. Sarah leaned back in the booth and crossed her arms over her chest, something he had noted long ago she did when uncomfortable or upset.

"He's going to get Chuck killed. That last mission would have killed him if we weren't there for back up." She said. Casey thought of that, more than he probably should have. He was glad that they were there.

"Maybe that's the point." He told her, looking away, not wanting to see her reaction to that. It was something he'd been thinking about more and more, something that made a lot of sense to him as a military man but probably not to a CIA Agent.

"What's that supposed to mean." She hissed out leaning forward. He was glad her hands were flat on the table or he'd be worried she'd skewer him with her knives.

"Exactly what I said walker." He stated as if it made perfect sense.

"That makes no sense Casey. Why would they go through all this trouble just to kill him?" She argued, voice rising slightly before she sat back abruptly looking around. He did the same, making sure nobody else heard her. Casey reached over and snatched the bottle of beer that Sarah had been playing with and took a long gulp, stalling before setting it down hard.

"It makes perfect sense Walker. Whatever you think, they don't know any more about this Intersect 3.0 than we do. This whole thing could blow up in their faces any day. " He told her, focusing intently into her eyes to show how serious he was. "They want to use their new toy in the best possible way as quickly as possible before its broken."

With that he dropped her gaze and lifted his glass towards the bartender. A moment later another whiskey was in front of him and he took a long sip from it. He didn't like that he had to say all that aloud. It made it all the more real and harder to pretend it wasn't happening. He cursed Chuck's name taking another drink for putting him in touch with that side of himself.

They didn't say anything for a long while. Sarah seemed lost in her own thoughts, thinking deeply on what he had just told her. He could tell that she never thought of the prospect that her agency would throw Chuck away so carelessly. He wasn't the only one who Bartowski changed. Out of the both of them Sarah had changed the most. Somehow Chuck took this broken little spy and put her back together. Compromised her beyond reason to the point where she would easily commit treason for him.

The intelligence community should find out how to bottle up whatever the hell Chuck Bartowski has that can compromise hardened Agents and use it as a weapon on enemy agents.

"What are we going to do Casey?" Sarah asked sadly. Glancing in her direction he wanted to run. Gone was the tough CIA agent and there sat a sad little woman who just wanted her love back. She seemed so fragile and broken, the complete opposite of what he was used to seeing. He wondered idly if this is what she looked like on the inside that Chuck had figured out and was fixing.

Sighing he sat back and raked his brain for something to say, anything to say. But he didn't know. He didn't have any answers. This was way over his head and he had no idea what to do except one thing and he wasn't ready to do that yet. It hasn't come to that yet.

"I don't know." He answered sullenly, drinking his whiskey.

The Intersect tiled Its head slightly as It stared out the bedroom window of Chuck Bartowski. It had been left alone for the most part for the past two days since their last briefing but It knew It wasn't truly alone. It was well aware that the cameras and audio equipment that littered the apartment Chuck shared with Agent Walker were turned on.

'Sarah.' It told Itself.

It watched as the strange little bearded man that Its records say were Morgan Grimes, best friend and part of Team Intersect, stood outside by the fountain uncertainly. It didn't know exactly who had been told about the upgrade to the Intersect, however It knew Its assignment was to maintain Chuck's cover and that would entail being friendly with this human.

With that in the forefront of Its temporal cortex the Intersect got up from the edge of the bed and went to the front door of the apartment, opening it up and startling the little man standing near it.

"Morgan." It said simply, watching as the man tried looking casual, but failing even to the Intersects eyes.

"Uh, Chuck, my main man. What is up?" He said looking around somewhat nervously. The Intersect tilted Its head again for a moment analyzing the situation. It wanted to put the man at ease and not frighten him. The man did live with Chuck after all and it would not do for the cover to be broken more than it already was.

"Morgan, are you going to come in?" It asked moving aside to let the man in. He watched curiously as Morgan glanced in the direction of Casey's apartment eagerly before taking a deep breath and smiling in his direction. He returned the gesture and held Its arm out to welcome him.

Following Morgan into the house, It watched as Morgan fidgeted for several moments, standing behind the couch and stood awkwardly.

"You know." He said simply, once again startling Morgan. Morgan shook his head nervously trying to dissuade him as the Intersect took a few steps closer to him. "Yes you do. You know I'm not Chuck."

"No no no. you're totally Chuck. Pfft, I don't know what you're talking about." Morgan stuttered taking a step back obviously scared. The Intersect put Its hand out in a calming manner, memories of clumsy Morgan moments filling Its mind and wanting to prevent another such occurrence, wondering if he knew he gave away his knowledge with his refutal.

"It's fine Morgan." He told him complacently. "Would you like to have a seat?"

They stared at each other for a few moments before Morgan walked the opposite way around the furniture to sit in the big chair by the back door. The Intersect took the seat opposite him, giving the man the space he obviously craved at the moment.

The Intersect watched Morgan carefully, analyzing his every move and cataloging it. Not because It felt threatened or for anything of real importance but out of curiosity. Ever since It became aware, the functions and habits of humans had fascinated and eluded It.

The first time It took over Chuck, when It first became fully aware, the functions It needed to instruct the various body parts surprised It. It had taken the Intersect several tries before It fully grasped the concept of moving Chuck's limbs. Everything was different being in control. Sights, smells, textures, everything was different than they were from being in the background of Chuck's mind.

It wasn't sure what to say to Chuck's best friend. Knowing the reactions of the others to Its presence, It could probably guess that It wasn't really wanted. They might not believe but the Intersect understood. It really did. They wanted their Chuck back; the Intersect didn't belong in this body. But they don't seem to understand that neither Chuck nor the Intersect had a choice in the matter.

Watching Morgan fidget for several minutes the Intersect wracked Its brain on some kind of idea on to get the man to settle down. It didn't want to make him feel so uncomfortable in his own home. The Intersect searched Its database for protocols for social interactions in humans, finally settling on an age old custom.

"Would you like a beverage of some kind?" It asked Morgan in a soothing voice. Morgan immediately stopped his fidgeting and stared back at him, blue eyes wide. Surprisingly not in fright.

"No, thank you Chu…uh…no. Thank you." He stumbled out causing the Intersect to once again tilt Its head.

"You may call me Chuck." It told him reassuringly, but Morgan's face went quickly from nervous to angry.

"I will not call you Chuck. You're not Chuck. You're a machine." He spat out sitting further on the edge of his seat. The Intersect gave a small smile, liking that this little gnome of a man would overcome his fear of It to defend his friend.

"I do not mean offense Morgan." The Intersect said placating, quirking the corner of Chuck's mouth. "Though I would like to point out I am in fact, a computer program, not a machine." It watched as Morgan's face soured.

"As if that matters!" With that Morgan stood up and walked around the couch heading for the back but stopped in his steps and turned around walking towards the Intersect. "Do you even have a clue what you've done? Does it even compute in your mind?"

The Intersect watched him, taking in his words, his demeanor. This Morgan was angry and the Intersect knew it, and It didn't blame him. He lost his best friend. The Intersect never had a friend, but knowing Chuck, feeling his feelings, watching his interactions, It knew what friendship was.

"I do." It told Morgan softly, turning away from the angry man's gaze to stare out the window. A little bird was sitting in the bird feeder that hung right outside and It couldn't stop the small smile that the bird brought to Chucks face.

This whole world fascinated It. Everything. From living things like birds and humans to inanimate objects like cups and TVs. It loved the feel of it all, the sense, the smell, the intrigue. The Intersect knew how everything functioned, how everything was made, created, put together, worked. But that didn't stop the intrigue of seeing in their final form, seeing them live and not as some schematic or file in Its mind.

So lost in Its own musings that the Intersect didn't see or hear Morgan move around the chair It was on and to sit on the couch next to It. It marveled at the feeling of being startled, never feeling that emotion before, always observant in Its environment. The Intersect looked at Morgan with a small smile still plastered on Chuck's face, feeling grateful to the little man for giving It that new feeling, though if It was honest with Itself, the feeling wasn't that pleasant.

They watched each other for several moments, wrapped in a comfortable silence. It could feel Morgan's eyes boring in to It, analyzing what he was seeing in front of him. It was fascinating to the Intersect to watch, always being the one doing the analyzing.

"You're not completely a machine are you? I mean, program. You feel!" Morgan said, voice rising slightly, thought the Intersect couldn't tell if it was in horror or excitement. It was silent for a moment while It contemplated Morgan's question.

"I do." It said simply. Morgan's mouth worked up and down a few times before a huge grin covered his face.

"That's amazing. I mean, really amazing. This is like something from a science fiction movie and honestly its very very terrifying but still, wow." He babbled, hands moving quickly around to emphasize his point.

"It's not so complicated." The Intersect replied. "I am programed to learn and grow. The makers thought it would be from my environment. What they didn't understand is I would first learn from my host." It told Morgan. It stopped, not sure if It should even continue. It wasn't sure why It felt like It could trust Morgan, or open up to him, but he'd been so lonely since Its emergence.

Morgan listened with rapt attention, eyes wide and fascinated. The Intersect felt comfortable with him, glad that for once it wasn't looks of derision, greed, or fear. It was fascinated by how Morgan processed his information, how his eyes would crinkle slightly and would move a little to the right, and his fingers twitched as if he were typing.

"Like a baby would first learn from its mother when born. I get it. You were a new born and Chuck was your mother. You learned from him!" He said excitedly as he figured it out. The Intersect couldn't help but smile at him, his cheerfulness being contagious. It liked these happy feelings.

But just like that Morgan's excitement died and he sat forward morosely staring at his hands for a few moments. The Intersects own smile died as well as he observed him, knowing already the cause of this.

"It's tragic you know." Morgan started, finally looking at the Intersect. "I don't know you, but so far, you've seemed nice so far. But, I really miss my friend." The Intersect looked away from him, staring at the TV for a moment before looking back.

"I understand. But Chuck, he's unavailable." It told Chuck's friend sadly. Looking closer at Morgan he saw his eyes moisten as tears began to form. It didn't want to see that, not after Sarah's tears the other day. They sat in silence again, each lost in their own thoughts. The Intersect thought perhaps he should just leave back to Chuck's room and leave Morgan to himself, but wasn't sure if that was the proper protocol.

A small sniffling sound came from the sofa and he turned to look back at Morgan seeing tears fall freely from his face. The Intersect knew what he was crying for. He was mourning the loss of his friend. The one who helped him, and stood by him, and grew with him his entire life. It could see it in Its mind's eye, as if it were the Intersect that was there and not Chuck.

"Is he really gone? For good?" Morgan asked so softly the Intersect almost didn't hear him. It thought for several moments on what to tell the man, not wanting to hurt him any further.

"It's an unknown science Morgan. Anything is possible." It said. Morgan sniffled loudly and coughed a few times as he gave a laugh.

"You, you are not what I expected. You're like him you know, from what I've seen. Kind, unassuming." But the Intersect shook his head against that, wishing that it were true. That he was as good as Chuck was, but he knew differently.

"Don't think that Morgan. Don't ever become complacent with me." He warned softly, hating that he had to warn this kind man. Morgan looked at him confused.

"I don't understand." He said. The Intersect stood up then from his place on the chair, towering over Morgan.

"I am a weapon Morgan. I was designed to follow orders by any means necessary. And if you were in my way of me completing it, I would not hesitate to kill you." It said seriously swallowing hard. "Never forget that."

With that the Intersect left Morgan there in the living room to himself and went to pack for his mission. One that hopefully will give him some answers on what he needs.

A/N: Ok next one probably next weds. Peace out. Please RR


	11. Chapter 11

A/N: Oh I'm so sorry for not posting. I had a messed up back and was sick for over a week and I'm finding writing this story very difficult.

Thank you to **BCC1, sevenrez, doc2or, uplink2, wilf21, Jimmy 144, ayleaa, Nomadic Nerd, **for your reviews. I really appreciate that you took time to read my story and give me feed back. **  
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And of course my beta **charahkids! **Who also encourages me to keep writing this thing.

Chapter 11

Mary Bartowski, AKA codename Frost sat back warily in her office chair looking over some surveillance video on her computer. She watched as her son, her baby boy entered an office building that Volkoff had been using in Poland for some deal he was working on and proceeded to thrash the office while killing anyone in his way.

She closed her eyes and shuddered at the image of Chuck covered in blood as he wrapped his arm around a woman's neck and quickly snapped it, killing her. After he dropped her body hard to the floor he turned towards the security camera that Mary was watching and stepped up to it, looking deep into its lenses giving her a complete view of his brown eyes. Eyes that she held in her memory as soft and caring, curious of the world around him, but were now dark and hard before he took out the camera.

Mary shut off the video, closing her eyes again momentarily hoping to wipe out the vision she had just seen. She hated the intersect project, always had. She was glad when her husband Stephen had given it up. But they both never dreamed that it would somehow find its way to their family, to their Chuck.

This was the exact reason Stephen left the program. He knew that someday someone would figure out how to take the information in the Intersect and have it over ride the users' mind, to effectively become a weapon, whose only real goal was to follow the orders of whoever had control of them.

Mary shuddered again, fully understanding what such an undertaking would involve on the person it was inflicted on. She had spent hours talking it over with Stephen, understanding the devastating effects it would have on the person. She lived with a walking example of it every day for the past twenty years.

Alexi Volkoff.

The CIA tested the first Intersect on him, to try to succeed in what had happened to Chuck only to have created a monster instead. Because of this, and the guilt her husband felt for allowing it to happen to his friend she had to leave her family, her life, and had been stuck for the past twenty years living in this hell following and watching over the maniac that took over their friend as he built one of the largest arms dealing networks in history.

She hated the thought but she wished many times she could just take him out and go home. But she knew her job was to take down the network, not the man. Plus she felt her husband's guilt at allowing his friend to be the test subject, and knew she wouldn't be able to just take him out.

The CIA had been horrified at the results of the test and had at first sent out a termination order. But after several failed attempts they began to see this as an opportunity like no other. A chance to get deep in the world of arms dealing and crime and be able to gather intimate details of all players that were out there. They were careful on who to take down, not wanting to put suspicion on a mole in Volkoff Industries but they kept tabs on everyone.

But it appeared that the CIA was done waiting now. That despite all the information they had gathered over the past twenty years from her as she went along with Alexi on this mission, that they were ready for it to end and start the cleanup. And they were doing it in the form of her son.

Volkoff had been pissed off at this latest development. He didn't know that they were sending her son to do the job. He didn't know that she had any children or a husband. The only thing he knew about this man was his name Agent Charles Carmichael. And this Carmichael was making him very nervous.

So far he had taken out seven of their business locations in the past three days, leaving none alive. Alexi had quickly scooped her from where she was at the time in Paris, brokering a deal for some components for some chemical agent Alexi was working on his own with, and had been brought immediately to Moscow to the main headquarters, where she now sat while watching surveillance from the other offices.

She wasn't sure what to do. She knew it was only a matter of time before Chuck would show up here and take out everyone, including herself. She was beyond pissed that the CIA had done this to her son. That after everything they've already done to her family that they would do this to him, and not warn her. If it weren't for her contacts within the CIA keeping tabs on her family all these years she wouldn't have known about this. The CIA would have just let Chuck murder her and have it be done without a second thought.

She knew what she had to do to fix it; there was no internal struggle for her as it would be for most other people. Stephen had developed a program that would erase the programing from the Intersect from the users mind.

The only problem was they weren't sure what condition they would be in afterwords. Having something overwrite one's mind is a dangerous thing and not something that should be taken lightly. She could only guess that was the reason Stephen hadn't used the program the first time the Intersect got downloaded into their sons head. He didn't want to risk his mind being that damaged.

But now there was no choice. Stephen was dead and she didn't trust anybody else who knew anything about the Intersect with her baby's mind. The program that Stephen had built to eventually get rid of the thing in Alexi's head would have to be used on Chuck. And she would have to do what she didn't want, and take out Alexi, because that had been Hartley's request. That if they couldn't remove it, then kill him.

The only question was how to get the program to Chuck.

Frost was interrupted from her thoughts by the beeping of her phone. She startled for a second before reaching to the table and picked it up. She listened to the panicked voice on the other end of the line as they warned her of an infiltration within the building that was heading to Volkoffs office.

Without responding she hung up the phone and reached into the desk grabbing the gun that lie there checking the mag before putting it in her waistband before reaching to the lower drawer and pulling out a tranq gun. She didn't want to hurt him but she had to somehow incapacitate him till she could retrieve the program.

Quickly she exited the room, walking down the hall at a fast stride. She bypassed the elevator and instead headed for the stairs to go up one floor to where Alexi's office was at, hoping to head Chuck off.

Exiting the floor and entering the hallway her foot slipped slightly on the pool of blood at the doorway from one of the guards that patrolled this floor. She glanced both ways of the hallway, noticing the line of bloody footprints that trailed from the elevator to Alexi's office.

She wasted no more time gawking and being horrified at the thought her child caused all this destruction and hurried down the hallway to the end where the door was opened wide. She sidled up next to the wall and glanced around the corner, seeing Alexi standing behind his desk, unarmed with a big grin on his face as he always did, stupidly not being scared out of his wits.

His voice floated out the door to her, hearing as he offered Chuck a position in his organization, seemingly impressed by his work thus far against him. However Chuck didn't even pause to consider it as he raised his gun swiftly and placed a bullet into Volkoffs forehead.

Mary froze, horrified at the sight. She was relieved that she wouldn't have to be the one to do the final act but she didn't want her son to be the one to do it either. She closed her eyes and took a deep breath, counting slowly in her head while she gripped the tranq gun.

"You can come out now Mary." Chuck's voice floated to her. Startled at being addressed her eyes popped opened alarmed and looked into the room. Chuck still stood facing the front of Volkoffs desk, not turning around. Letting out the breath she didn't know she was holding she slowly let go of the wall she was pressed against and waked slowly into the room.

"How did you know?" She asked him hesitantly, holding the gun tighter. She heard his intake of breath before he turned around, his own eyes closed. Her finger twitched on the trigger wanting to take advantage of the moment but couldn't bring herself yet to do so. She watched cautiously as he opened his eyes and a small smile spread upon his face.

"You smell the same. That same lotion or soap that you always used. Vanilla and cinnamon with just a little hint of something else I never was able to identify. But it was always distinctly you."

Mary paused stunned at his confession. It was the only thing that she kept with her that she continually kept using from her former life. It was small and easy to acquire more of as her husband sent it as a mail order package. The memories of her children held in her arms, buried deep into her body as they inhaled the scent they loved so much was the one thing she refused to give up.

"It's a tropical flower." She told him coming out of her stupor, taking a cautious step closer, curious on what was going on. "It's very rare but your father created it just for me."

"Chuck's father was a very intelligent man." It said, boring its gaze into her. She nodded her head, giving herself a second to think.

"You speak of yourself in the third person Chuck." She said plainly, deciding to take the direct approach. Her son at the moment was very dangerous and lingering in his presence too long could be very dangerous and by all the video she's seen, deadly. She looked up at him and watched as he analyzed her and it made her feel self-conscious.

"I am not Chuck Mary. You know that. You are well aware of what I am." It told her.

"I do." She said simply walking closer to him before side stepping around him to look over the desk. Alexi Volkoff's body laid there on his back, arms laid out and a grin still on his face while his blood seeped out from the wound on his forehead. She felt sadness grip her heart at seeing he former friend and companion of the past twenty years put to death like that. But in their line or work there really was no better alternative. He was destined to have an unpleasant death.

"So, my son." She started, giving one last glance at Volkoff before turning back towards Chuck. "Is he dead?" She watched his facial features closely but he gave nothing away

"Does it really matter Mary? You left him twenty years ago. You gave up the right to be concerned about his wellbeing long ago." It told her coldly, surprising her at how personal it seemed to take her abandonment.

"He is my son and I will always be concerned for his wellbeing. Regardless of how long I've been out of his life." She told him honestly.

The Intersect smirked at that, somehow finding it all amusing, though what It found so amusing Mary was unsure about. Her finger twitched again on the trigger, her whole body telling her to just lift her arm already and knock him out. That she didn't have time to play this exchange right now.

"I wouldn't do that Mary." The Intersect warned, yet again startling her. She mentally shook her head and told herself to get into the game. She never would let her guard down like this if it were anyone else.

Mary looked up at him, seeing the glint in his eyes obviously knowing what she was going to do, but raising no defense against her. She wondered if she really wasn't a threat to him or if the Intersect in her sons head was really just that cocky. But she raised the tranq gun anyways, pointing it directly at him, not surprised in the slightest that he didn't even blink.

"What are you going to do with that Mary?" It asked her calmly, staring directly at her, ignoring the gun on him.

"I'm going to take you someplace safe and try to get my son back." She told him, frowning when his smirk got bigger.

"So there is a way isn't there? I knew there was. I found the information in my data, but not a location, and not if it was ever completed." Her stance loosed slightly at the excitement that seemed to radiate off him. It confused her, expecting a different emotion if any at all.

"Yes there is a way." She told him.

"But it's risky isn't it?" His smirk fell then and he glanced at the gun for a second before looking back at her. "I can't let you do that Mary."

With that he quickly stepped forward grabbed her arm pushing it up just as she pressed on the trigger releasing the darts from inside. He grabbed the gun from behind her back with his other arm as he kicked her knee causing her to fall forward and snagging the tranq gun from her as she fell.

Mary collapsed on the ground on her hands and knees, body throbbing slightly from the exertion, still unaware fully of what just happened. She looked up from her spot, glaring angrily up at the man that was her son, and cursing herself for hesitating.

"What are you going to do now Chuck? Are you going to kill me?" She spat out angrily, but the Intersect shook his head and tossed the guns on the table. Reaching down he pulled her up by her arms and pressed her against the desk hard, towering over her. He was close enough that she could feel his warm breath push aside the loose strands of hair from her forehead and she debated if she could get out of the hold.

"You are going to tell me about this program. Where is it?" He said angrily at her. Mary refused to back down and met him gaze for gaze as she struggled out of his tight hold.

"I won't tell you anything. I won't let you take away my son's only chance to be free." She spat angrily at him. The Intersect held on tighter and she let out a moan in pain as she felt the pressure on her arms build leaving harsh bruises. He brought his lips close to her ear and she closed her eyes afraid.

"You will take the chance to muddle his mind and kill Chuck. I will not allow that. I will live, I will protect him." He pulled back then and threw her hard to the floor. She felt a break in her wrist break as she landed hard on the ground.

She grasped her wrist and groaned in pain, but didn't let it distract her. She looked up at him, confusion filling her face as she eyed him warily.

"What do you mean protect him? You mean yourself." She argued trying to get up onto her knees. The smirk came back to the Intersects face as he reached down and grabbed her arm again, helping her up.

"We are the same are we not Mary. We share the body. The program would damage the mind, regardless of whom or what was in control." He led her roughly over to the couch that Volkoff had on one side of the room and roughly pushed her down. "You're intentions are noble but unwise. You would hurt your son more than help."

"I'd rather see him dead then be a prisoner forever." She told him as he released her arm. The Intersect gave a small laugh, once again startling her.

"You presume too much about the situation Mary. But don't worry." He walked away from her and reached the tranq gun that lay on the desk and pointed it at her. "I'll take care of the situation."

With that, she felt to stings in her chest and looked down in time to see two darts sticking out of her before she lost consciousness. Her last vision was of her son leaning forward and the feeling of his hand as he brushed aside her hair.

Several hours, a plane ride with an inflight debrief and a rented car speeding down the highway in the middle of the night had Mary in Burbank on her way to her daughter's residence. She felt her nerves bubble up within her making her feel ill but she stamped it down and ignored it the best she could.

She always dreamed of the day she would be able to come back to her children, and hopefully their father. But not like this. Not with her loving husband dead, murdered by a man in passion of an Intersect. And not with her son being taken over by the Intersect.

She cursed Stephens name under her breath. She loved him dearly, beyond anything other than her children, but the whole Intersect project he had created and assembled had done nothing but ruin their lives. It's been a plague on the family. He lost his life to it and now she was afraid she may have lost her son as well to this thing.

Mary slowed down as she reached her exit, driving carefully down the quiet street. She looked around the neighborhood as she drove; saddened at seeing where her children had ended up. It was a nice location for sure, considering they live more towards the city and not in the suburbs where she had left them. It was a nice neighborhood, with nice apartment buildings, parks, and small shops scattered along the main ways.

It was a beautiful place and she was sure, no she knew, from the reports she received over the years that her children were happy where they were. But she had wanted to keep them safe, locked away in the house they grew up in. Where she could keep an eye on them herself more often via the surveillance she and Stephen had set up before she left.

Mary allowed her thoughts to linger on that for a moment longer as she finally pulled into the enclosed community that her children lived in and blew out a long breath. This would be the first time in twenty years that she will see her daughter face to face. To finally see her face to face in the flesh and not as some image she had received. To finally be able to tell her daughter how proud she is of her, of how she stepped up to the plate and raised Chuck so well and still fulfilled her own dreams.

Taking a deep breath Mary finally exited her car, quietly closing the door on it and walked up to the gated entry. She looked up in the corners, knowing of the video surveillance and audio bugs littering the whole courtyard courtesy of John Casey, NSA. She knew if he was home he would be aware of her presence by now, that she probably tripped some silent alarm that would activate and alert him to an intruder coming into the courtyard at two in the morning.

She walked further in, taking her time looking around, admiring how beautiful the place was with its twinkling lights and outdoor fireplace. How the fountain, now turned off for the night simmered clear and fresh in its tiers.

Glancing to the left she noted there was a light on in a bedroom of where her son lived. His bedroom. She wondered if he was in there, having succeeded in finishing his mission if it was only to take out Volkoff or if it was Sarah Walker, CIA Agent and apparent love of Chuck's in there mourning his loss.

She wanted to go there and find out, quail her curiosity but she had something more important to do at the moment, and in any case both Sarah and Casey will most likely be there in no time anyways once her daughter no doubt alarms them of her presence.

Walking up to the front door she took a few deep breaths. She wanted to kick herself for feeling like this; she was a trained spy that had been deep undercover for over twenty years with one of the world's biggest arms dealers and sociopaths. Yet the thought of finally seeing Ellie frightened her.

Taking one last breath she raised her arm and knocked firmly on the door and waited. All the lights were off in the apartment signaling that they had already gone to bed at that time so she waited patiently, counting to thirty quietly in her head before knocking once more.

After what felt like an eternity a light was turned on in the front room and she heard footsteps walk heavily to towards the door. She braced herself for whoever was opening it, probably armed with some large object due to the time of night it was.

The door opened slowly at first then wider as a tall man with blond hair and a very nice muscled chest opened the door and looked down at her with sleepy eyes. She gave a wan smile up at him, finally getting the first real look at her son-in-law.

"May I help you ma'am?" He asked politely as his frame blocked the room beyond from view. She was about to open her mouth to speak her first words to the man that had stolen her daughters heart when she heard Ellies voice float out from behind him.

"Devon, who is it?" Ellies sleepy voice said as she walked up behind him and placed a hand on his back. Mary watched as Ellie peaked around her fit husband at the person at the door, and braced herself further as she watched her jaw drop open in shock. "Mom?" She stuttered out quietly.

Mary gave her a small smile and forced herself to keep her tears at bay for the moment.

"Hello Eleanor." She replied.

A/N: So the bad news is, I'm still not feelin the story. I'm so glad many of you are enjoying it. The good news is, I don't believe in abandoning a fic, so never fear! It will be completed. But just so you know I'm going to try to wrap this up in the next 5 chapters.

Peace out yo!

Missy


	12. Chapter 12

A/N. This chapter, was a complete NIGHTMARE to get up. Let me just say, i've had it sitting here in front of me for 2 hours trying to get it posted but things just keep refreshing or messing up. So I hope you enjoy it. Thank you all who reviewed, i'd post your names but i'm afraid this chapter wont let me.

Thanks to charahkids for being my Beta. I swear any mistakes you see is not from them, its from me. I went back to edit after I got the mistakes but it kept effing up so I had to do it 4 or 5 times and by the last time I just said "eff it"

Chapter 12

If you had asked Sarah Walker what she had planned for the evening, sitting in the Woodcomb's apartment at 3AM would not have been on the list. She had taken advantage of the Intersect being out of town on whatever mission the CIA sent him on and gone back to their apartment for the time.

The first time she entered their room after he had left she had stood there for an indeterminate amount of time glancing around, using her honed spy skills to notice if anything was missing or out of place. Even though the thing was inhabiting Chuck's body she couldn't bare for the thing controlling him touching Chuck's stuff. Playing with it, moving it, enjoying or even analyzing the items. Once she was satisfied that everything was how they left it she immediately collapsed on the bed, curling up in a fetal position and let herself cry again.

In the back of her head she could hear Agent Walker telling her to stop sniveling and get up, but she ignored her, something that actually felt good. That feeling made her cry harder. She was becoming more human, more alive and the person who was responsible for it, who she wanted to experience it with, was not there with her. Was not there to celebrate it or mourn the loss.

She eventually got herself up and began the long arduous task of assisting Ellie and Devon in researching some kind of possible fix for Chuck. However, no matter how many hours they spent on the task, they were no closer with coming up with any idea on how to help him. It seemed impossible. There was no research on this subject, or at least nothing viable in the realm of reality. There were plenty in the sci-fi fantasy world but nothing viable in reality.

She had stayed up late that night going over yet another medical journal and had fallen asleep at Chuck's computer desk when she was abruptly woken up by the ringing of her phone next to her head. She had groaned in pain before answering it and hearing Ellie's voice on the other end telling her to come over and quickly had caused her spy senses to kick in and she immediately went over.

To say she was surprised to see Mary Bartowski, Chuck's long gone mother would be an understatement. Entering the apartment of her best friend and seeing the woman sitting in a chair by the fireplace with a mug of coffee was as much a shock to her as it probably was for Ellie. However the older woman didn't really show the surprise, or even any glimmer of happieness. If anything, she looked more pissed.

They waited several more minutes for Casey and Morgan to arrive. Devon flitted around the room getting people coffee and making sure they were alright. Casey of course was a delight as always. He was always ready for anything, however when woken up with no action, well, it tended to make him a little extra grumpy. But she didn't pay him any mind, instead she sat in a large comfortable chair at the end of the couch facing the door, watching the woman who had hurt her boyfriend as she sipped from her mug.

And that is where she now sat, in their living room surrounded by everyone who cares about Chuck. The tension was thick with Mary Bartowski there. There was so much Sarah wanted to say to her, both pleasant and not. She wanted to get to know the woman who had birthed the man that she was madly in love with while at the same time interrogate her on how she could abandon the two most important people in her life.

Despite what she wanted to say and what she shouldn't say, Sarah knew it was nothing in comparison to what Ellie must be feeling. She could tell by the strained look on her face as she sat next to her husband on the couch, clutching his hand tightly, showing that she had the same desire to ask questions as Sarah did, obviously more so.

Sarah thought about what it would be like if it were her own mother, who had abandoned her so long ago as well. What if it were her that showed up one night out of the blue. Her first instinct would to be angry, righteously so. To show that she had done well on her own and hadn't needed her. That she was fine and her abandonment hadn't hurt her as much as it did.

On the other hand she would want nothing more than to throw her arms around her and hold her tight and close afraid of letting her go again. To sob into her shoulder the pain and frustrations she'd had growing up without her and tell her how much she had needed her.

Sarah watched Ellie close wondering which way she would go. Would she choose the strong path or embrace her mother's return? Sarah didn't know, she couldn't guess. Ellie was as much a mystery as she was an open book, but Sarah knew whichever way she went she would be there to support her.

"Enough of this crap. Its three AM, who are you and what are you doing here." Casey finally barked out to the woman, giving her his most harden glare. To her credit Mary didn't flinch or cower away. She just glanced up at him momentarily before returning her eyes back to Ellie.

"I have information for you. Information that could possibly save Chuck." She said simply as she took a sip from the coffee mug she held in her hands. Sarah watched as she closed her eyes momentarily appreciatively, wrapping her fingers tightly around the hot mug and enjoyed the warm liquid that entered her. It was a curious tell she thought. Thinking that wherever this woman had been hiding all these years it was probably cold.

"Bartowski is fine." Casey denied crossing his arms over his large chest. Mary set her mug down and sitting up straighter, placing her hands together in her lap she looked around.

"How about we just cut through all the crap and be straight." She said, causing Sarah's curiosity to peak.

"That's a great idea mom. How about we start with what you are doing here. You leave for twenty years then just show up in the middle of the night claiming to have information on something? Where have you been since I was twelve?" Ellie asked angrily sitting up from her reclined state. Devon held her hand tightly and tried pulling her back.

Mary watched Ellie cautiously, a frown forming on her face. Sarah couldn't help but notice the similarity of it to both Chuck and Ellie, causing a slight twinge of ache to pulse inside her, suddenly wanting to see the woman smile. To see if it looked like Chuck's.

"I understand your pain Eleanor but-"

"Oh, you understand? You understand what it was like to be abandoned by your mother and father and left to raise your teenaged brother? To have to worry and panic over everything from food, to school, to chores when I should have been worrying about football games and prom dresses. You understand?" Ellie shouted getting emotional.

"Eleanor, there is a lot you don't know about." Mary said patiently, sitting further on the edge of her chair.

"That's because you left us without an explanation!" With that Ellie ripped her hand from her husbands and stood up to walk around the couch. Sarah stood up from her own space she was occupying, keeping in between the two in case Ellie got to emotional and tried to physical.

"You said you have information on Chuck. How could you?" Sarah finally cut in, stopping any further outburst from happening. She understood how upset Ellie was and she believed she had a right to her answers but right now there was something more pressing. She watched as Mary's brow crinkled in concern and stared at Sarah, as if sizing her up.

"I know about the Intersect. I know that Chuck has it." She said.

"How could you…I mean. We have no idea what you're talking about." Morgan blurted out before correcting himself. Sarah rolled her eyes and wondered once again why Morgan was even there. She knew when he caught her heading over that she shouldn't have told him but she couldn't help but think him part of the team. Chuck did.

"Shut it Grimes." Casey muttered out glaring at him with cold eyes. But Mary just bristled it all away and motioned Morgan to come sit by her. He hopped over the coffee table away from Casey and sat on the floor right next to her, astounding Sarah. This woman abandoned his best friend when they were kids and he just did what she said.

"Morgan!" Sarah hissed out sharply. He looked up at her confused and she rolled her eyes again.

"We don't have time for this. I know about it because of Stephen, my husband. He created it." Mary started. "He informed me several years ago that it had somehow got to Chuck and that he had it."

"Wait, you were in contact with dad? This whole time? You two leave us and yet you stay in communication with each other?" Ellie said coming forward again, only to be blocked by Casey's large hand as he blocked her path.

"Yes Eleanor, we did. It was not easy to leave you kids you have to believe that." She pleaded. Ellie crossed her arms over her chest and glared at the woman who gave her life.

"I don't have to believe anything. I don't owe you anything, but you do owe me and Chuck an explanation." She bit out.

"How about we get a little less interruption and a lot more information hmm?" Casey barked out, stepping in between the women. Sarah watched as Ellie turned around and headed around the sofa again, beginning to pace. A trait she shared with Chuck when he was feeling frustrated or had something on his mind.

"Long story short I was on a long term deep under cover mission. I work for the CIA." Mary finally said.

"No way Mrs. B! That's so-"

"Grimes!" Casey growled. Morgan immediately shut up and cowered back a bit behind the chair Mary was on. Much to Sarah's surprise and amusement she reached out and ran her hand in circles on his back making calming noises before looking up and glaring at Casey. If it were any other situation Sarah might have laughed out loud, however the seriousness of it kept her Agent mask in place.

"Don't be a bully Col. Casey." Mary admonished, not breaking eye contact.

"Either you tell us what you know or I'll show you what a bully is." He threatened stepping closer. However Mary seemed unconcerned with him and just returned his glare.

"As I was saying, my cover was as the right hand person for Alexi Volkoff." She began again.

"Then why aren't you there instead of here? Why come back now?" Sarah asked her. She moved closer to the chair that Mary was in and sat on the edge of the couch.

"My mission just ended abruptly." She paused, breathing in deep. "They sent Chuck to close the OP up. He took down the biggest locations of Volkoffs business, including his home base in Moscow. Including him."

"So Volkoffs dead? About damn time." Casey grunted out his approval, though Sarah could tell by the way he held himself straighter that he didn't like the fact that Chuck was the one to do it.

"It was, amazing to watch. He was unstoppable. I must confess it's the first time in a long time that I was frightened." She said.

"So you've seen him? You've seen Chuck?" Sarah asked eagerly, putting together the pieces. Knowing now what the mission was they sent him on without them frightened her now. Hearing what he had done as Mary explained made her sickened and sad. For the first time since this all started, as she listened to Mary tell her tale of destruction brought on by Chuck she found herself hoping that If Chuck was in there that he couldn't see it. That he wasn't a witness to this, to all the death and disorder the Intersect caused his body to make. She hoped that he was gone.

"That is absolutely amazing. Chuck took down an entire bad guy infrastructure in three days in various countries, all by himself." Morgan said mouth opened, eyes wide amazed, making Sarah angry.

"It wasn't Chuck, Morgan. It was the Intersect. Chuck would never do something like that." She bit out angrily, refusing to let Chuck get dragged into all this. Chuck was innocent in this.

Well, it's a little bit Chuck. I mean, the body is, and some of his personality is." He defended, not put out by her tone.

"What do you mean, 'personality'" Ellie asked finally calming down and sitting next to Sarah. Everyone watched Morgan expectantly as he bit on his inside cheek thinking.

"Just that, when I spoke to him the other day, he well, he was like Chuck."

"It's a machine Morgan, it's not Chuck. It's programed to assimilate into his life and take over." Sarah explained, losing patience with Chuck's best friend. But Morgan shook his head in disagreement.

"It's not a machine, Sarah. It's a program. A program that was created and built to learn from its environment. And what was his first environment?" He said with wide eyes.

"Chuck." Ellie whispered covering her mouth in horror. Sarah watched her face as her eyes moved back and forth quickly as she thought of what Morgan had said and seemed to be analyzing it.

"Dude." Devon stated breaking the thick silence as he fell heavily into the chair Sarah had recently vacated. Sarah narrowed her eyes looking back and forth between both of them, getting annoyed at being left out of the loop.

"What? What is it?" She said, trying to gain their attention. Ellie lowered her arm slowly from her mouth and looked next to her at Sarah. "What is it Ellie?"

"Chuck." She said simply as if that should explain everything but Sarah was still lost after thinking about it.

"You're going to have to elaborate Ellie." She said, trying to sound more patient then she felt.

"I think Chuck's alive." She stated, a smile coming across her face. Sarah looked over at Casey who shrugged his shoulders just as confused.

"How?" Sarah asked her.

"What Morgan said. It's a program that's created to learn from its environment. According to you it took several uploads before it was fully operational. Its first environment was Chuck. It learned everything from him." Ellie said excitedly.

"But how does that make Bartowski alive?" Casey asked.

"Because Chuck is a good person."

"I should have stayed in bed." Casey grumbled out walking away towards the kitchen for more coffee.

"Don't count it out bro, it makes sense." Devon cut in, coming to his wife's defense. Sarah watched astonished as Casey chugged down and entire mug of hot coffee in three seconds before refilling his cup and coming out.

"So tell me. What in hells name does Bartowski being a good person equal up to him being alive?" Casey intoned coming back into the living room.

"That's an easy answer big guy!" Morgan said standing up and clearing his throat. "I'll take it from her Ellie dear." He told her and walked around the chairs and couch over to where Casey stood. Casey took one glance at Morgan before rolling his eyes and growling, taking a couple steps away from him.

"Fine genius, you explain it then." He growled into his mug.

"I wish I could take credit for this my friend but sadly know. This is from the horse's mouth himself so to speak. Chuck was the programs first environment. It was in there for several weeks just clawing at Chuck's brain. It would have learned how to act, or feel whatever from Chuck." He explained.

Sarah sat back on the couch facing forward taking silent breaths as she thought about that. She wished now more than ever that she had paid more attention to whenever Chuck nerded out on a computer program or whatever so she could understand better what was going on.

"Ok." She started sitting up and turning around on the couch getting on her knees. "Say that's true, then why is it doing what it does. It's killing people, a lot of people. It goes on missions with guns and weapons and explosives, everything that Chuck is against."

Sarah closed her eyes then not wanting them to show how this Intersect had gotten under her skin. That she was bothered by all of this, though there was no doubt that everyone already knew. She felt Ellie lean against her and she opened her eyes and looked into the soft brown orbs that were so similar to Chucks as she gave her a small smile.

"Hey." She said softly bumping her shoulder against her gently. The single word and gentle bump soothed her and calmed her the way it did whenever Chuck would do it. Something about their presence just always seemed to calm her down, wipe away the frenzied feelings.

Sarah returned the small smile and bumped her back with her hip before turning back to Morgan with a piercing stare, giving him her full attention with an open mind. She watched as Morgan crossed his own arms around his chest self-consciously as everyone eyed him, waiting for some kind of explanation but the little guy didn't seem to have one.

"Well…" Devon interrupted the silence that had eclipsed the room causing all attention on him. Being the awesome guy he was however it didn't seem to bother him at all. "It is still a program. It was created to learn and grow but it still has its core programing. Which is to follow orders. If those orders are to kill than…"

She heard Mary sigh and turned back around on the couch to watch her as she thought; biting her lip on the corner in the same way as her children did when they were thinking over something. Analyzing some detail into little bits and pieces.

"Yeah but it did seem to ignore some kind of order that was implanted in it. It's protecting Chuck." Mary told them. "Or at least that's the impression I got when It inquired about the program."

Sarah's breath hitched as she listened. Chuck Alive. She knew it was a possibility, its what they were banking on but she never really allowed herself to hope or even dream that it could possibly be true. But hearing possible proof from both Morgan and this woman, his mother who showed up out of no where, it just further caused her to think on it.

Shaking her head to erase the thought. She wouldn't allow her hopes to get up. Yes she wanted Chuck alive, but it hurt too much to even hope for it. But it made more sense now, hearing it from others. She remembered how the Intersect spoke, how It avoided direct answers when about Chuck. She thought it was odd then but now it makes sense. That perhaps the Intersect had grown attached to Chuck, knew that someone wanted to get rid of him and was protecting him.

Mary stood up from her chair and began pacing around the room. She couldn't pin point why but for some reason the action made Sarah nervous and on edge. She was a trained CIA Agent who was an unknown to her up until about an hour ago. She didn't like that she was walking around freely, looking around the room, taking stock of the surrounding, picking up photos around the room scrutinizing the faces within.

She glanced over at Casey and felt some small amount of relief as she noticed him surveying Mary as well, not letting her out of his sight. Sarah felt a tinge of regret in her gut at thinking of Chuck's mother as a threat. But that's what she was. She left her children twenty years ago for a mission, and in Sarah's book that made you almost as low as the dirt bags they fight to put away.

This whole situation had made Sarah think more and more about both the future and the past. About what she wanted out of her life and what she wanted to avoid. Before Chuck the only thing she could see was the present, the CIA and surviving another mission.

Now after Chuck came barreling into her life, now she saw a future. A life outside the CIA with a family, with Chuck. Now with Mary here, it drew up her old feelings of abandonment from her own mother, and hearing it was for a CIA mission just made her even madder. She may have understood at one point how Mary could make such a decision, but now, she couldn't even fathom it. Couldn't imagine leaving behind her family the way Mary did. And at that moment, she felt all the anger and hurt that she knew Chuck felt but never showed her regarding his mother's disappearance.

No she didn't trust Mary Bartowski, not at all. But she was desperate to get Chuck back and as much as she hated to admit it, his mother may be able to help them.

"Well this is all well and good information but none of this is going to help Chuck. Just because we have a better understanding doesn't get us closer to a solution." Ellie said morosely, burying her face into the pillow from the couch. Sarah reached out and rubbed small circles on her back soothingly, agreeing whole heartedly with her.

Mary came round the couch one more time and returned to the chair she had vacated not too long ago, sitting stiffly on the edge, hands back in her lap as she leaned forward tensely.

"There may be one way." She said softly, gaining everyone's attention. Ellie sat up immediately removing the pillow and glared angrily at her.

"And you're just mentioning this now? We've been sitting here for over an hour!" She shouted. But Mary just shook her head gently.

"Because it's very risky. I can't give you much detail but there is a program that Stephen had developed to get the Intersect programing out of a person's head. It's never been tested for obvious reasons but it could be the only chance we have to get that thing out of his head." She told them seriously.

Sarah stared hard at her, trying to see if there was any kind of deception in her expression. She didn't see any and her heart sped up at the prospect of possibly having a chance to save Chuck.

"What kind of risk? What does this program do exactly?" Ellie, always the doctor and protector of her little brother inquired, sitting up straighter herself. Mary paused before answering hesitantly.

"What it's meant to do is cancel and delete the Intersect posting from the persons mind. But doing so could very well delete a lot of information from the hosts mind as well." She took a breath before she turned her gaze on Ellie. "It could also over stimulate his mind and cause more permanent damage."

"As in…" Sarah asked, already knowing the answer, but still needing it said out loud. Ellie sighed and closed her eyes a moment before answering her.

"As in, if it doesn't kill him it could very well leave him brain damaged." She said softly.

Sarah's breath hitched at the implications, wondering to herself if that would be better for him. She didn't know. She had spent all this time fighting to get Chuck back that she didn't think of the implications of what it would cause on Chuck's mental being.

"I'm aware of the risks mother. And I'm prepared for them. We need to get our hands on that program, and we need to use it on Chuck." Ellie stated firmly.

Sarah turned in her seat and gaped at her in horror. She couldn't believe what she was hearing. Didn't want to. She watched horrified as Devon got up from his chair opposite them and came to sit next to Ellie, grabbing onto her hands in show of support.

"What?" Sarah stuttered out stunned. "You can't be serious Ellie? The risk is too high. Chucks brain could be turned to Mush. He...he could lose everything that he is."

"He's already losing everything he is Sarah. Don't you see it?" Ellie argued, still using her logical voice she used when she was in doctor mode. Something that was suddenly starting to piss Sarah off.

"You can't do that to him. There has to be another way Ellie. Doing this, it's giving up on him." Sarah stated desperately, but she watched as Devon squeezed Ellie's hand tightly, and she knew she wasn't going to win this battle. Tension rose in the room between them and began suffocating Sarah. Her mind was telling her to flee, to leave, but her heart told her to stay there and fight.

Finally after the silence stretched out for several minutes Ellie turned her body on the couch to face Sarah, her eyes soft yet still stern, still in control.

"I understand how you feel Sarah. But this is my brother. I am his family. His only real family." Ellie bit out giving her mother a hard glance before turning back to Sarah. "Devon and I, we've discussed this and this is our decision."

Sarah gave a laugh of derision before standing up, needing to get away from Ellie before she lashed out and took her out.

"Your decision? Your decision is to take a chance on your brother's mind and destroy it. Make him and keep him something than what he is." She argued, her breath hitching as an ache took over her body.

"It's a better choice than what you would do." Ellie bit out angry, surprising everyone one in the room. It was no surprise that Ellie was protective of her brother but she had never actively gotten angry at Sarah. The tension in the room kicked up a few notches and in her peripheral Sarah saw Casey stiffen up ready for action if needed. Taking a few calming breaths Sarah mentally shook out her thoughts and met Ellies eyes.

"And what is that supposed to be? " She asked her, not really wanting to know the answer.

"Please, cut the crap Sarah Walker. I'm not dumb. Remember? I raised him. And Morgan as well to some extent." She said crossing her arms and glancing at Morgan who wisely had taken a few steps back behind Casey as the two girls argued.

"What does-"

"One of his stupid pacts with Morgan. They agreed that if either of them was taken over by a cyborg or zombie apocalypse or some sort of nonsense the other would make sure to take the other out or some kind of crap like that. It was complete bullshit until it came true, and he happened to come across two spies who have the abilities to fulfill his wish." Ellie explained looking back and forth between Sarah and Casey.

Sarah kept her lips terse, not saying a word. It was a ridiculous pact she recognized but she couldn't deny the truth of it. Sarah knew she should say something, deny it vehemently, but the look in Ellies eyes told her it would be a waste, that she whole heartedly believe that Chuck would stick to that and ask the two trained spies and assassins to not make him live like that. Apparently Casey's silence had verified her suspicion.

"I thought so." She said after a moment. "So our choices is either kill him out right or take the only chance we have and see if we can save him. "

"But will he really be saved Ellie? With his mind destroyed. Who knows how he'll end up? For all we know it'll turn him into a vegetable or worse. I know Chuck; I know he wouldn't want to live like that either Ellie."

"Yeah well, luckily you don't get a say in the matter." Ellie shouted back at her stunning Sarah. Sarah's mouth opened a closed a few times before she shut it firmly. The words hit her like a brick wall and every part of her hurt. She couldn't look away from Ellie whose features were still hard but her eyes were softening, and Sarah knew that she didn't mean the words so harshly.

Casey stepped forward then in between the two girls, standing closer to Sarah than Ellie figuring that she would be the one who would need restraining If need be.

"That's enough of this." He barked out annoyed. "It's pointless either way at the moment. For now let's focus on obtaining the program. We'll figure out what to do then." He gave Sarah a piercing look, telling her to get herself together and think like an Agent. She gave a slight nod of her head indicating she understood his message.

Mary stood up then as Devon walked behind Ellie and placed his hands on her shoulder rubbing them gently. Sarah felt a pang of jealousy at seeing them, wishing that Chuck was there to do the same to her. To calm her and sooth her, to be on her side instead of her feeling like she's finding by herself.

It was then that she noticed that Morgan had moved forward as well, standing behind Casey next to her. She had to fight the tears that threatened to come out at the moment, her emotions were flying too high at the moment and she really needed to punch something, and hard.

But the small show of solidarity towards her in the way Morgan seemed to be near her did comfort her and calm her a bit. And knowing how much he adored Ellie and probably agreed with her since it was his pact he made, just made the small gesture a little more special to her.

"Alright you'll need to retrieve the program. Get me a map and I'll show you where it is."

A/N: Alright, few more chapters. I'm sure its predictable where this is going. I already have a good idea (i hope good) for my next story. Once this is done with. Till next time!


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